Attempting to run using mpirun consistently fails, even using provided test data with call provided in the manual.

This is the only error message passed to the cluster job handler.
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 16

I don't know what else to provide, I've been struggling to get this software to work for over 12 hours today. Completely exhausted and stumped. Is there a google group or something? I have found nowhere else to post this.

In meta.cpp and utils.cpp, the function strcasecmp is non-portable. This prevents me from building modeltest on Windows. Would it be possible to use an alternative -- for example, converting optarg to lowercase in meta.cpp, or converting tmpchar to uppercase in utils.cpp?

Hi,

I got error 'Segmentation fault (core dumped)' while running command as below:

./modeltest-ng -d nt -i my_alignment.fasta -o myco_model -p 20 -q modeltest.txt -r 1000000 -t ml -m JC,HKY,TrN,TPM1,TPM2,TPM3,TIM1,TIM2,TIM3,TVM,GTR

May I know what is this error about and how to fix it? Thanks.
myco_modeltest.txt
concatenated_core_gene_alignments_myco_trimal.fasta.txt

I tried to run Modeltest-ng on a PHYLIP interleaved formated file. I got the error message:
modeltest-ng: Cannot parse the msa: in.phy
[910]: Sequence 1 (T1) longer than expected

I converted the input MSA into a PHYLIP sequential formated file and Modeltest-ng ran succesfully.

Is there a chance for the next Modelttest-ng release to support PHYLIP interleaved formated MSA?

It would be desirable that given the same input data, ModelTest should always produce the same results regardless the selected parallelization approach. Not only the best-fit model selection, but also the same likelihood scores and therefore model/partitioning selection scores.

However, using different starting parameters (model parameters + topology + branch lengths) to the optimization of each candidate substitution model has a significant effect on the execution time, but can also affect the final log-likelihood, parameter values and thus the selection process itself. One can expect, for example, the alpha shape parameter to be similar between +G models, or the proportion of invariant sites between +I models. In order to accelerate the model parameter optimization, keeping the optimal parameter values from one model to another seems to be a good approach (to the extent possible, given the model constraints).

Nevertheless, when using different high level parallelization schemes (task level) the sequence in which the models are optimized might be different and also the starting parameters. The problem arises when the results of the optimization differs according to the starting parameter values, and not only the execution times. There are several possible solutions:

1. Use fixed starting parameters (e.g., alpha = 0.5, pinv = 0.0, substitution rates = {1.0, 1.0, 1.0, 1.0, 1.0, 1.0}). Reproducibility is guaranteed but slows down the optimization process considerably.
2. Take one single model parameters as starting point for the rest (e.g., GTR+G, JTT+G). Reproducibility is guaranteed but delays the task level parallel execution until the first model is optimized.
3. Somehow do a quick and good estimation of the starting model parameters. Is this possible for every parameter?
4. Keep the parameters between models for each execution thread (by thread here I mean a thread or a process that sequentially optimizes a subset of candidate models). Speeds up the process, but the results might not be exactly reproducible if more than one single thread is used (because of the dynamic distribution of models to the threads).

4b. If the candidate models are distributed statically among threads, the results will be reproducible as long as the same number of execution threads are used, but this can increase the workload imbalance.

Hi Diego and all,

I am running modeltest-ng 0.1.5 on a quite large alignment.
As suggested by Diego, I split the partition file into 10 subfiles and started 10 separate jobs (although I don't think it's related to my issue), to fit the memory.
All the 10 jobs failed on the same assertion:

modeltest-mpi: ../src/model/parameter_gamma.cpp:100: double modeltest::ParameterGamma::optimize(modeltest::mt_opt_params_t *, double, double, bool): Assertion     `!loglh || (cur_loglh - loglh)/loglh <= 1e-10' failed.

I recently successfully ran modeltest-ng on the same dataset with the same splitting strategy. The only difference is that I added the models LG4M and LG4X to the analysis that failed.

Any idea about what could be wrong? If yes, is there any quick workaround I could use? (like removing or relaxing the assert)

Cheers,
Benoit

Command line:

modeltest-ng-static -i nido_wolftrim.afa -d aa -p 10

Downloaded today, release v0.1.6, version modeltest x.y.z according to --version

Alignment and log posted here:

https://drive5.com/tmp/nido_wolftrim.tar.gz

Implement Kuhner-Felsenstein branch score difference and Decision Theory

Dear Diego,

I am running modeltest on a big protein MSA (~300,000 sites, 1344 species, ~1000 partitions) on supermuc.

I managed to treat one third of the partitions on 20 nodes within the wall time.
Then I resubmitted the exact same job, but it crashes with error 137 (usually out of memory error).
The ckp file is 20Go big.

Cheers,
Benoit

Hi Diego,

Modeltest-ng does not support some phylip files that raxml-ng supports (see original issue and example alignment here: https://groups.google.com/forum/#!topic/raxml/n7-NiVepOgw).

This is because libpll offers two functions (pll_phylip_parse_sequentialand pll_phylip_parse_interleaved) that parse two different kind of phylip files, but you only try the first one: https://github.com/ddarriba/modeltest/blob/master/src/msapll.cpp#L420

If you don't have the time to fix it, I can also submit a pull request next week.

Greetings from Heidelberg ;-)
Benoit

Hi Diego,

A ParGenes user (in case you don't know about it, ParGenes is a parallel pipeline that calls modeltest-ng and raxml-ng) got the following error in one modeltest run:

Integer divide by zero at address 0x803F4E883
==22315==    at 0x4493AA: modeltest::Model::evaluate_criteria(unsigned int, double) (model.cpp:393)

Here is the problematic fasta file. I had to change the extension otherwise github reject it:
fasta.log

I reproduced using the dev branch with:

modeltest-ng -i fasta.log -t mp

Cheers
Benoit

Not sure what this error means:
modeltest: algo_search.c:925: pllmod_algo_spr_round: Assertion `fabs(loglh - best_lh) < 1e-6' failed.

modeltest aborts after this

Good afternoon,

I was following the instructions for building modeltest-ng using cmake from the tarball, but it seems the tarball does not include the necessary files in pll-modules. The specific error during the build is:

[  3%] Generating ../localdeps/lib/libpll.a
/bin/sh: /home/brant/src/modeltest-0.1.5/libs/pll-modules/install-with-libpll.sh: No such file or directory
make[2]: *** [localdeps/lib/libpll.a] Error 127
make[1]: *** [libs/CMakeFiles/libpll.dir/all] Error 2
make: *** [all] Error 2

Checking out the source (and submodules) fixes the issue, but this does not seem to be the expected behavior of a build from the tarball (as far as I can tell).

command: modeltest-ng −i faa/OG0001.aln

error messages:
modeltest: Cannot parse the msa:
[900]: input file does not exist
modeltest: You must specify an alignment file (-i)
Error: Invalid arguments
Try modeltest --help for more information

Why the warning happened and how to fix it?

modeltest-ng -i ALL.core.protein.fasta.gb -t ml -o modeltest_aa -p 15 -d aa

Physical cores: 72
Logical cores: 144
Memory: 1.01e+03GB
Extensions: AVX

WARNING: Partition DATA: Sequences 09_Feb and DSM_26881 are identical
WARNING: Partition DATA: Sequences 19A_GOM_1509m and 23_GOM_1509m are identical
WARNING: Partition DATA: Sequences 19A_GOM_1509m and Choline_3u_9 are identical
WARNING: Partition DATA: Sequences 22501_18_FS and 22507_15_FS are identical
WARNING: Partition DATA: Sequences ACAM_239 and ACAM_246 are identical
WARNING: Partition DATA: Sequences ACAM_239 and ACAM_255 are identical
WARNING: Partition DATA: Sequences BZ_SZ_XJ27 and BZ_SZ_XJ27T are identical
WARNING: Partition DATA: Sequences CGMCC_1_6773 and JCM_14802 are identical
WARNING: Partition DATA: Sequences DSM_16096 and FP35 are identical
WARNING: Partition DATA: Sequences MA_ZP17_13 and YYYZ_3 are identical
WARNING: Partition DATA: Sequences NRS2HaP1 and R57_5 are identical
WARNING: Partition DATA: Sequences PA5 and TA22 are identical
WARNING: Partition DATA: Sequences PA5 and TA6 are identical
WARNING: Partition DATA: Sequences SYSU_XM8 and SYSU_ZJ2214 are identical
WARNING: Partition DATA: Sequences Soap_Lake__6 and Soap_Lake__7 are identical
WARNING: MSA has not enough sites to infer reliable results
Creating new checkpoint file: modeltest_aa.ckp

When I run "modeltest-ng.exe --version" (compiled on Windows) some information about the version is printed twice to the console:
_ _ _ _ _ _ _____
| | | | | | | | \ | |/ |
_ __ ___ ___ __| | | | | ___ | | | | | | __
| ' _ \ / _ \ / _ |/ _ \ | __/ _ / __| _| | . ` | | | |
| | | | | | () | (| | / | || /_ \ | | |\ | || |
|| || ||___/ _,|_||__||/_| || _|____|

ModelTest-NG v0.1.7 released on 17.03.2021 by The Exelixis Lab.
Written by Diego Darriba.
Contributors: Tomas Flouri, Alexey Kozlov, Benoit Morel, David Posada,
Alexandros Stamatakis.
Latest version: https://github.com/ddarriba/modeltest

ModelTest-NG v0.1.7 released on 17.03.2021 by The Exelixis Lab.
Written by Diego Darriba.
Contributors: Tomas Flouri, Alexey Kozlov, Benoit Morel, David Posada,
Alexandros Stamatakis.
Latest version: https://github.com/ddarriba/modeltest

Modeltest manual says in 5.4:

• DATA TYPE can be DNA or PROTEIN
Modeltest code says in https://github.com/ddarriba/modeltest/blob/master/src/utils.cpp#L591:
else if (!strcasecmp(tmpchar,"PROT") || !strcasecmp(tmpchar,"AA"))

Also, it would be nice to have an example of the partition scheme file format in the wiki or in the examples.

Hi Diego,

you provide a very useful parameter --template.
Unfortunately, it does not support raxml-ng yet (or does raxml correspond to raxml-ng?)

Is it possible to add it?

Best,
Benoit

Hello,
I get an error because 2 or more genes overlap. For example, here ATP8 and ATP6.
Is there a way I can force modeltest-ng to keep the partitions as is or do they need to be consecutive?
Thank you so much!!!!
Karla

DNA, ATP8 = 8022-8186
DNA, ATP6 = 8177-8860
DNA, COIII = 8860-9643
DNA, ND3 = 9644-9995
DNA, ND4L = 9996-10292
DNA, ND4 = 10286-11663

Error:
[error] modeltest-ng: Error in partitions file: partition-file.txt
[error] [10402] Partition ATP6 overlaps another partition
Error: Invalid arguments

sudo apt install flex

bison might also be required but I didn't test it. I also installed that while I was installing flex. After that, instructions in README.md worked

I tried several of the ways to compile described in the Wiki (cmake, autotools, script...) each failing for one reason or another, finally trying "Compiling manually (Linux and OS X)" from here: https://github.com/ddarriba/modeltest/wiki/Download-and-Install

I succeeded with 1) libp11
When trying to build the p11-modules starting with autoreconf -i and ./configure I get

...
checking pll.h usability... no
checking pll.h presence... no
checking for pll.h... no
configure: error: pll.h not found

The packages libp11-dev and p11-kit-dev are installed, in case that makes a difference.

Using modeltest-ng v0.1.2 static 64bit Linux binary (downloaded from releases at GitHub), running on:

$ uname -a
Linux <MACHINE_NAME> 2.6.32-696.18.7.el6.x86_64 #1 SMP Thu Jan 4 17:31:22 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

with the command:

$ modeltest-ng/modeltest-ng -T raxml -i PF14200/nt_backtrans.trimal.1.fasta

and the attached data: nt_backtrans.trimal.1.fasta.txt (.txt extension only to get GitHub to allow upload)

I see the error:

Partition 1/1

    1/24   JC             0h:00:00   0h:00:01           -4488.8506       -       -
    2/24   JC+I           0h:00:00   0h:00:01           -4466.1916       -  0.0208
    3/24   JC+G           0h:00:00   0h:00:01           -4366.1397  1.6524       -
    4/24   JC+I+G         0h:00:00   0h:00:01           -4363.1826  1.9105  0.0200
    5/24   F81            0h:00:00   0h:00:01           -4486.9120       -       -
    6/24   F81+I          0h:00:00   0h:00:01           -4462.7894       -  0.0208
    7/24   F81+G          0h:00:00   0h:00:01           -4355.4930  1.5209       -
    8/24   F81+I+G        0h:00:00   0h:00:01           -4352.1043  1.7593  0.0200
    9/24   K80            0h:00:00   0h:00:01           -4471.1617       -       -
   10/24   K80+I          0h:00:00   0h:00:01           -4448.2561       -  0.0208
modeltest-ng: binary_io_operations.c:109: binary_update_header: Assertion `next_block < bin_header.max_blocks' failed.

but I don't understand the reason for failure. With the verbose flag, the error reported is:

Partition 1/1

    1/24   JC             0h:00:00   0h:00:01           -4488.8506       -       -
    2/24   JC+I           0h:00:00   0h:00:01           -4466.1916       -  0.0208
    3/24   JC+G           0h:00:00   0h:00:01           -4366.1397  1.6524       -
    4/24   JC+I+G         0h:00:00   0h:00:01           -4363.1826  1.9105  0.0200
    5/24   F81            0h:00:00   0h:00:01           -4486.9120       -       -
    6/24   F81+I          0h:00:00   0h:00:01           -4462.7894       -  0.0208
    7/24   F81+G          0h:00:00   0h:00:01           -4355.4930  1.5209       -
    8/24   F81+I+G        0h:00:00   0h:00:01           -4352.1043  1.7593  0.0200
    9/24   K80            0h:00:00   0h:00:01           -4471.1617       -       -
[dbg] Building parameters and computing initial lk score
[dbg] Initial log likelihood: -4917.97
[dbg] final parameter optimization: -4917.97
[dbg] fix branches -4499.17
[dbg] optimize BranchLengths: -4499.17
[dbg] optimize P-inv: -4499.17
[dbg] optimize Frequencies: -4499.17
[dbg] optimize Alpha: -4499.17
[dbg] optimize SubstRates: -4450.49
[dbg] fix branches -4448.38
[dbg] optimize BranchLengths: -4448.38
[dbg] optimize P-inv: -4448.38
[dbg] optimize Frequencies: -4448.38
[dbg] optimize Alpha: -4448.38
[dbg] optimize SubstRates: -4448.33
[dbg] fix branches -4448.26
[dbg] optimize BranchLengths: -4448.26
[dbg] optimize P-inv: -4448.26
[dbg] optimize Frequencies: -4448.26
[dbg] optimize Alpha: -4448.26
[dbg] optimize SubstRates: -4448.26
[dbg] fix branches -4448.26
[dbg] optimize BranchLengths: -4448.26
[dbg] optimize P-inv: -4448.26
[dbg] optimize Frequencies: -4448.26
[dbg] optimize Alpha: -4448.26
[dbg] optimize SubstRates: -4448.26
[dbg] model done: [0.01/0.0001]: -4448.26
[dbg] Model optimization done: -4448.26
   10/24   K80+I          0h:00:00   0h:00:01           -4448.2561       -  0.0208
modeltest-ng: binary_io_operations.c:109: binary_update_header: Assertion `next_block < bin_header.max_blocks' failed.
Aborted (core dumped)

Thank you in advance for your help.

L.

Hi, I encountered some error messages as I tried to install the program via cmake on terminal.

The error messages came after the "make" command:
bash-3.2$ make
Scanning dependencies of target libpll
[ 3%] Generating ../localdeps/lib/libpll.a
/bin/sh: /Users/babu/Desktop/modeltest-master/libs/pll-modules/install-with-libpll.sh: No such file or directory
make[2]: *** [localdeps/lib/libpll.a] Error 127
make[1]: *** [libs/CMakeFiles/libpll.dir/all] Error 2
make: *** [all] Error 2

I've tried other ways to install it but all failed at certain point.
I am new to this environment. Please help me out. Thanks.

Implement LG4 mixture models in protein model selection

Hello Diego,

I have a multiple alignment of 3000 bacterial genomes. Full alignment is about 5 Mb long, but only 50k sites are polymorphic (about 20k are AGCT only). Should I use full alignment or polymorphic sites only to determine the best model? Thank you in advance.

Hi,

I got an error as below:

modeltest: Error in partitions file: /home/umhir/Desktop/Planococcaceae8_coregene.txt
[10401] Partition WP_04969456 is out of bounds
Error: Invalid arguments

The alignment contains 298053 nt, and partition is defined as below:

DNA, WP_04969456 = 58207-59484\3
DNA, WP_04969456 = 58208-59484\3
DNA, WP_04969456 = 58209-59484\3

May I know what can I do to fix the error? Thanks.

Hi!

I'm trying to install jmodeltest-ng and I obtained this error:
Using Qt version 5.6.2 in /Users/BEHB/anaconda/bin/lib
...configuration:
prefix: /modeltest/modeltest-0.1.3/build
build: /modeltest/modeltest-0.1.3/build
pll: [yes] /modeltest/modeltest-0.1.3/libs/pll-modules/libs/libpll
modules: [yes] /modeltest/modeltest-0.1.3/libs/pll-modules
include: /modeltest/modeltest-0.1.3/build/include
lib: /modeltest/modeltest-0.1.3/build/lib

...writing log to /modeltest/modeltest-0.1.3/build.log
...build pll
...building pll
...pll FAIL!

when I do ./build.sh

hi
i had encountered some problems when i build ModelTest-NG using cmake,

configure: error: could not find required installation of BISON
make[3]: *** No rule to make target 'install'。 停止。
libs/CMakeFiles/libpll.dir/build.make:60: recipe for target 'localdeps/lib/libpll.a' failed
make[2]: *** [localdeps/lib/libpll.a] Error 2
CMakeFiles/Makefile2:85: recipe for target 'libs/CMakeFiles/libpll.dir/all' failed
make[1]: *** [libs/CMakeFiles/libpll.dir/all] Error 2
Makefile:83: recipe for target 'all' failed
make: *** [all] Error 2
i look forward to your help

Implement tree distances.

For example, DT criterion is based on topological distances. Hence it makes no sense to compute it with fixed topologies.

I'm having errors in installation. I'm using MacOS Catalina. If anyone can help, it'd be much appreciated! Here's my build.log:

configure arguments: CPPFLAGS=-I/Users/macair/modeltest/build/include LDFLAGS=-L/Users/macair/modeltest/build/lib --prefix /Users/macair/modeltest/build
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... ./install-sh -c -d
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... rm: conftest.dSYM: is a directory
yes
checking dependency style of gcc... gcc3
checking whether ln -s works... yes
checking how to run the C preprocessor... gcc -E
checking for main in -lm... yes
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking libpll/pll_binary.h usability... yes
checking libpll/pll_binary.h presence... yes
checking for libpll/pll_binary.h... yes
checking libpll/pllmod_algorithm.h usability... yes
checking libpll/pllmod_algorithm.h presence... yes
checking for libpll/pllmod_algorithm.h... yes
checking libpll/pll_optimize.h usability... yes
checking libpll/pll_optimize.h presence... yes
checking for libpll/pll_optimize.h... yes
checking libpll/pll_tree.h usability... yes
checking libpll/pll_tree.h presence... yes
checking for libpll/pll_tree.h... yes
checking for pthread_create in -lpthread... yes
checking cassert usability... yes
checking cassert presence... yes
checking for cassert... yes
checking climits usability... yes
checking climits presence... yes
checking for climits... yes
checking cstdin usability... no
checking cstdin presence... no
checking for cstdin... no
checking fstream usability... yes
checking fstream presence... yes
checking for fstream... yes
checking iomanip usability... yes
checking iomanip presence... yes
checking for iomanip... yes
checking iostream usability... yes
checking iostream presence... yes
checking for iostream... yes
checking map usability... yes
checking map presence... yes
checking for map... yes
checking string usability... yes
checking string presence... yes
checking for string... yes
checking vector usability... yes
checking vector presence... yes
checking for vector... yes
checking for stdbool.h that conforms to C99... no
checking for _Bool... no
checking for inline... inline
checking for size_t... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working strtod... yes
checking for floor... yes
checking for mkdir... yes
checking for pow... yes
checking for sqrt... yes
checking for strrchr... yes
checking for strtol... yes
checking for mpic++... mpic++
checking for MPI_Init... yes
checking for mpi.h... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating mpi/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands
/Library/Developer/CommandLineTools/usr/bin/make all-recursive
Making all in src
g++ -g -O3 -Wall -L/Users/macair/modeltest/build/lib -o modeltest-ng genesis/modeltest_ng-date_time.o genesis/modeltest_ng-string.o genesis/modeltest_ng-logging.o modeltest_ng-static_analyzer.o service/modeltest_ng-modeltestservice.o service/modeltest_ng-checkpoint.o thread/modeltest_ng-observer.o thread/modeltest_ng-parallel_context.o model/modeltest_ng-abstract_parameter.o model/modeltest_ng-parameter_branches.o model/modeltest_ng-parameter_ratecats.o model/modeltest_ng-parameter_gamma.o model/modeltest_ng-parameter_pinv.o model/modeltest_ng-parameter_substrates.o model/modeltest_ng-parameter_frequencies.o model/modeltest_ng-model.o model/modeltest_ng-dnamodel.o model/modeltest_ng-protmodel.o optimize/modeltest_ng-model_optimizer_pll.o optimize/modeltest_ng-partition_optimizer.o modeltest_ng-model_selection.o modeltest_ng-modeltest.o modeltest_ng-msapll.o modeltest_ng-partition.o modeltest_ng-partitioning_scheme.o modeltest_ng-treepll.o modeltest_ng-utils.o modeltest_ng-meta.o modeltest_ng-main.o -lpll_binary -lpll_algorithm -lpll_optimize -lpll_msa -lpll_tree -lpll_util -lpll -lpthread -lm
Undefined symbols for architecture x86_64:
"___emutls_v.pll_errmsg", referenced from:
ModelTestService::topological_summary(std::vector<unsigned int, std::allocator > const&, modeltest::ModelSelection const&, modeltest::ModelSelection const&, modeltest::ModelSelection const&, std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::basic_ostream<char, std::char_traits >&) in modeltest_ng-modeltestservice.o
modeltest::Checkpoint::ckp_load_model(modeltest::Model&) in modeltest_ng-checkpoint.o
modeltest::Model::input_bin(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in modeltest_ng-model.o
modeltest::ModelOptimizerPll::ModelOptimizerPll(modeltest::MsaPll&, modeltest::TreePll&, modeltest::Model&, modeltest::Partition&, bool, unsigned int) [clone .cold] in modeltest_ng-model_optimizer_pll.o
modeltest::eval_ckp(mt_options_t&, modeltest::selection_instance*) in modeltest_ng-modeltest.o
modeltest::MsaPll::initialize(bool) in modeltest_ng-msapll.o
modeltest::MsaPll::test(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&, unsigned int*, unsigned int*, unsigned int*, msa_format_t*, data_type_t*) in modeltest_ng-msapll.o
...
"___emutls_v.pll_errno", referenced from:
modeltest::Checkpoint::ckp_save_model(modeltest::Model const&) in modeltest_ng-checkpoint.o
modeltest::Checkpoint::ckp_load_model(modeltest::Model&) in modeltest_ng-checkpoint.o
modeltest::ParameterBranches::optimize(modeltest::mt_opt_params_t*, double, double, bool) in modeltest_ng-parameter_branches.o
modeltest::ParameterGamma::optimize(modeltest::mt_opt_params_t*, double, double, bool) in modeltest_ng-parameter_gamma.o
modeltest::ParameterPinv::optimize(modeltest::mt_opt_params_t*, double, double, bool) in modeltest_ng-parameter_pinv.o
modeltest::Model::output_bin(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) const in modeltest_ng-model.o
modeltest::Model::input_bin(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) in modeltest_ng-model.o
...
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make[2]: *** [modeltest-ng] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

OS: ArchLinux
Installing: rename the binary from the relase.

[root@helix bin]# ./modeltest-ng
Illegal instruction (core dumped)

It's okay for my other machies.

Hi,
I tried to upgrade and install all required package to allows a smooth install with cmake, but I always get an error at the make step. I also get an error with autotools version. I copy/paste terminal output during install with cmake (it seems this strategy fails close to the end).
I am on ubuntu 14.05 with biolinux 8 distro.

jean-baptiste@jeanbaptiste-HP-Z640-Workstation[modeltest] mkdir build && cd build
jean-baptiste@jeanbaptiste-HP-Z640-Workstation[build] cmake .. [ 4:14]
-- The C compiler identification is GNU 4.9.4
-- The CXX compiler identification is GNU 4.9.4
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Compier: GNU
-- Building DEBUG
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Using flags: -std=c++11 -Wall -Wextra -DPTHREADS -pthread -D_NO_GUI_
-- Building dependencies in: /home/jean-baptiste/modeltest/build/localdeps
-- Configuring done
-- Generating done
-- Build files have been written to: /home/jean-baptiste/modeltest/build
jean-baptiste@jeanbaptiste-HP-Z640-Workstation[build] make [ 4:14]
Scanning dependencies of target libpll
[ 3%] Generating ../localdeps/lib/libpll.a
aclocal: installing 'm4/libtool.m4' from '/usr/share/aclocal/libtool.m4'
aclocal: installing 'm4/ltoptions.m4' from '/usr/share/aclocal/ltoptions.m4'
aclocal: installing 'm4/ltsugar.m4' from '/usr/share/aclocal/ltsugar.m4'
aclocal: installing 'm4/ltversion.m4' from '/usr/share/aclocal/ltversion.m4'
aclocal: installing 'm4/ltobsolete.m4' from '/usr/share/aclocal/ltobsolete.m4'
libtoolize: putting auxiliary files in .'. libtoolize: copying file ./ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIR, m4'. libtoolize: copying file m4/libtool.m4'
libtoolize: copying file m4/ltoptions.m4' libtoolize: copying file m4/ltsugar.m4'
libtoolize: copying file m4/ltversion.m4' libtoolize: copying file m4/lt~obsolete.m4'
configure.ac:17: installing './compile'
configure.ac:11: installing './config.guess'
configure.ac:11: installing './config.sub'
configure.ac:6: installing './install-sh'
configure.ac:6: installing './missing'
src/Makefile.am: installing './depcomp'
configure.ac: installing './ylwrap'
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 3458764513820540925
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @file support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for flex... flex
checking lex output file root... lex.yy
checking lex library... -lfl
checking whether yytext is a pointer... yes
checking for bison... bison -y
checking for exp in -lm... yes
checking assert.h usability... yes
checking assert.h presence... yes
checking for assert.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking stdio.h usability... yes
checking stdio.h presence... yes
checking for stdio.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking ctype.h usability... yes
checking ctype.h presence... yes
checking for ctype.h... yes
checking x86intrin.h usability... yes
checking x86intrin.h presence... yes
checking for x86intrin.h... yes
checking for inline... inline
checking for size_t... yes
checking for uint32_t... yes
checking for int64_t... yes
checking for uint64_t... yes
checking for uint8_t... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working alloca.h... yes
checking for alloca... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for asprintf... yes
checking for memcpy... yes
checking for memset... yes
checking for posix_memalign... yes
checking for ps2pdf... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating man/Makefile
config.status: creating examples/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands

libpll 0.3.2

Target:    linux-gnu x86_64
Compiler:  gcc
CFLAGS:    -g 
LIBS:      -lm  

Continue with 'make' command

Making install in src
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-fasta.lo -MD -MP -MF .deps/libpll_la-fasta.Tpo -c fasta.c -fPIC -DPIC -o .libs/libpll_la-fasta.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-fasta.lo -MD -MP -MF .deps/libpll_la-fasta.Tpo -c fasta.c -o libpll_la-fasta.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-gamma.lo -MD -MP -MF .deps/libpll_la-gamma.Tpo -c gamma.c -fPIC -DPIC -o .libs/libpll_la-gamma.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-gamma.lo -MD -MP -MF .deps/libpll_la-gamma.Tpo -c gamma.c -o libpll_la-gamma.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-likelihood.lo -MD -MP -MF .deps/libpll_la-likelihood.Tpo -c likelihood.c -fPIC -DPIC -o .libs/libpll_la-likelihood.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-likelihood.lo -MD -MP -MF .deps/libpll_la-likelihood.Tpo -c likelihood.c -o libpll_la-likelihood.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-list.lo -MD -MP -MF .deps/libpll_la-list.Tpo -c list.c -fPIC -DPIC -o .libs/libpll_la-list.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-list.lo -MD -MP -MF .deps/libpll_la-list.Tpo -c list.c -o libpll_la-list.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-maps.lo -MD -MP -MF .deps/libpll_la-maps.Tpo -c maps.c -fPIC -DPIC -o .libs/libpll_la-maps.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-maps.lo -MD -MP -MF .deps/libpll_la-maps.Tpo -c maps.c -o libpll_la-maps.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-models.lo -MD -MP -MF .deps/libpll_la-models.Tpo -c models.c -fPIC -DPIC -o .libs/libpll_la-models.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-models.lo -MD -MP -MF .deps/libpll_la-models.Tpo -c models.c -o libpll_la-models.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-pll.lo -MD -MP -MF .deps/libpll_la-pll.Tpo -c pll.c -fPIC -DPIC -o .libs/libpll_la-pll.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-pll.lo -MD -MP -MF .deps/libpll_la-pll.Tpo -c pll.c -o libpll_la-pll.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-output.lo -MD -MP -MF .deps/libpll_la-output.Tpo -c output.c -fPIC -DPIC -o .libs/libpll_la-output.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-output.lo -MD -MP -MF .deps/libpll_la-output.Tpo -c output.c -o libpll_la-output.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-utree.lo -MD -MP -MF .deps/libpll_la-utree.Tpo -c utree.c -fPIC -DPIC -o .libs/libpll_la-utree.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-utree.lo -MD -MP -MF .deps/libpll_la-utree.Tpo -c utree.c -o libpll_la-utree.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-rtree.lo -MD -MP -MF .deps/libpll_la-rtree.Tpo -c rtree.c -fPIC -DPIC -o .libs/libpll_la-rtree.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-rtree.lo -MD -MP -MF .deps/libpll_la-rtree.Tpo -c rtree.c -o libpll_la-rtree.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-derivatives.lo -MD -MP -MF .deps/libpll_la-derivatives.Tpo -c derivatives.c -fPIC -DPIC -o .libs/libpll_la-derivatives.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-derivatives.lo -MD -MP -MF .deps/libpll_la-derivatives.Tpo -c derivatives.c -o libpll_la-derivatives.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-partials.lo -MD -MP -MF .deps/libpll_la-partials.Tpo -c partials.c -fPIC -DPIC -o .libs/libpll_la-partials.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-partials.lo -MD -MP -MF .deps/libpll_la-partials.Tpo -c partials.c -o libpll_la-partials.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-compress.lo -MD -MP -MF .deps/libpll_la-compress.Tpo -c compress.c -fPIC -DPIC -o .libs/libpll_la-compress.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-compress.lo -MD -MP -MF .deps/libpll_la-compress.Tpo -c compress.c -o libpll_la-compress.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-utree_moves.lo -MD -MP -MF .deps/libpll_la-utree_moves.Tpo -c utree_moves.c -fPIC -DPIC -o .libs/libpll_la-utree_moves.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-utree_moves.lo -MD -MP -MF .deps/libpll_la-utree_moves.Tpo -c utree_moves.c -o libpll_la-utree_moves.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-utree_svg.lo -MD -MP -MF .deps/libpll_la-utree_svg.Tpo -c utree_svg.c -fPIC -DPIC -o .libs/libpll_la-utree_svg.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-utree_svg.lo -MD -MP -MF .deps/libpll_la-utree_svg.Tpo -c utree_svg.c -o libpll_la-utree_svg.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-parsimony.lo -MD -MP -MF .deps/libpll_la-parsimony.Tpo -c parsimony.c -fPIC -DPIC -o .libs/libpll_la-parsimony.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-parsimony.lo -MD -MP -MF .deps/libpll_la-parsimony.Tpo -c parsimony.c -o libpll_la-parsimony.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-core_derivatives.lo -MD -MP -MF .deps/libpll_la-core_derivatives.Tpo -c core_derivatives.c -fPIC -DPIC -o .libs/libpll_la-core_derivatives.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-core_derivatives.lo -MD -MP -MF .deps/libpll_la-core_derivatives.Tpo -c core_derivatives.c -o libpll_la-core_derivatives.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-core_partials.lo -MD -MP -MF .deps/libpll_la-core_partials.Tpo -c core_partials.c -fPIC -DPIC -o .libs/libpll_la-core_partials.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-core_partials.lo -MD -MP -MF .deps/libpll_la-core_partials.Tpo -c core_partials.c -o libpll_la-core_partials.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-core_pmatrix.lo -MD -MP -MF .deps/libpll_la-core_pmatrix.Tpo -c core_pmatrix.c -fPIC -DPIC -o .libs/libpll_la-core_pmatrix.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-core_pmatrix.lo -MD -MP -MF .deps/libpll_la-core_pmatrix.Tpo -c core_pmatrix.c -o libpll_la-core_pmatrix.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-core_likelihood.lo -MD -MP -MF .deps/libpll_la-core_likelihood.Tpo -c core_likelihood.c -fPIC -DPIC -o .libs/libpll_la-core_likelihood.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-core_likelihood.lo -MD -MP -MF .deps/libpll_la-core_likelihood.Tpo -c core_likelihood.c -o libpll_la-core_likelihood.o >/dev/null 2>&1
updating parse_utree.h
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-parse_utree.lo -MD -MP -MF .deps/libpll_la-parse_utree.Tpo -c parse_utree.c -fPIC -DPIC -o .libs/libpll_la-parse_utree.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-parse_utree.lo -MD -MP -MF .deps/libpll_la-parse_utree.Tpo -c parse_utree.c -o libpll_la-parse_utree.o >/dev/null 2>&1
updating parse_rtree.h
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-parse_rtree.lo -MD -MP -MF .deps/libpll_la-parse_rtree.Tpo -c parse_rtree.c -fPIC -DPIC -o .libs/libpll_la-parse_rtree.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-parse_rtree.lo -MD -MP -MF .deps/libpll_la-parse_rtree.Tpo -c parse_rtree.c -o libpll_la-parse_rtree.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-lex_utree.lo -MD -MP -MF .deps/libpll_la-lex_utree.Tpo -c lex_utree.c -fPIC -DPIC -o .libs/libpll_la-lex_utree.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-lex_utree.lo -MD -MP -MF .deps/libpll_la-lex_utree.Tpo -c lex_utree.c -o libpll_la-lex_utree.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-lex_rtree.lo -MD -MP -MF .deps/libpll_la-lex_rtree.Tpo -c lex_rtree.c -fPIC -DPIC -o .libs/libpll_la-lex_rtree.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-lex_rtree.lo -MD -MP -MF .deps/libpll_la-lex_rtree.Tpo -c lex_rtree.c -o libpll_la-lex_rtree.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-fast_parsimony.lo -MD -MP -MF .deps/libpll_la-fast_parsimony.Tpo -c fast_parsimony.c -fPIC -DPIC -o .libs/libpll_la-fast_parsimony.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-fast_parsimony.lo -MD -MP -MF .deps/libpll_la-fast_parsimony.Tpo -c fast_parsimony.c -o libpll_la-fast_parsimony.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-stepwise.lo -MD -MP -MF .deps/libpll_la-stepwise.Tpo -c stepwise.c -fPIC -DPIC -o .libs/libpll_la-stepwise.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-stepwise.lo -MD -MP -MF .deps/libpll_la-stepwise.Tpo -c stepwise.c -o libpll_la-stepwise.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-random.lo -MD -MP -MF .deps/libpll_la-random.Tpo -c random.c -fPIC -DPIC -o .libs/libpll_la-random.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-random.lo -MD -MP -MF .deps/libpll_la-random.Tpo -c random.c -o libpll_la-random.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-phylip.lo -MD -MP -MF .deps/libpll_la-phylip.Tpo -c phylip.c -fPIC -DPIC -o .libs/libpll_la-phylip.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-phylip.lo -MD -MP -MF .deps/libpll_la-phylip.Tpo -c phylip.c -o libpll_la-phylip.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-hardware.lo -MD -MP -MF .deps/libpll_la-hardware.Tpo -c hardware.c -fPIC -DPIC -o .libs/libpll_la-hardware.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-hardware.lo -MD -MP -MF .deps/libpll_la-hardware.Tpo -c hardware.c -o libpll_la-hardware.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-repeats.lo -MD -MP -MF .deps/libpll_la-repeats.Tpo -c repeats.c -fPIC -DPIC -o .libs/libpll_la-repeats.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -g -MT libpll_la-repeats.lo -MD -MP -MF .deps/libpll_la-repeats.Tpo -c repeats.c -o libpll_la-repeats.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -mfma -mavx2 -g -MT libsimd_avx2_la-core_partials_avx2.lo -MD -MP -MF .deps/libsimd_avx2_la-core_partials_avx2.Tpo -c core_partials_avx2.c -fPIC -DPIC -o .libs/libsimd_avx2_la-core_partials_avx2.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -mfma -mavx2 -g -MT libsimd_avx2_la-core_partials_avx2.lo -MD -MP -MF .deps/libsimd_avx2_la-core_partials_avx2.Tpo -c core_partials_avx2.c -o libsimd_avx2_la-core_partials_avx2.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -mfma -mavx2 -g -MT libsimd_avx2_la-core_derivatives_avx2.lo -MD -MP -MF .deps/libsimd_avx2_la-core_derivatives_avx2.Tpo -c core_derivatives_avx2.c -fPIC -DPIC -o .libs/libsimd_avx2_la-core_derivatives_avx2.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -mfma -mavx2 -g -MT libsimd_avx2_la-core_derivatives_avx2.lo -MD -MP -MF .deps/libsimd_avx2_la-core_derivatives_avx2.Tpo -c core_derivatives_avx2.c -o libsimd_avx2_la-core_derivatives_avx2.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -mfma -mavx2 -g -MT libsimd_avx2_la-core_pmatrix_avx2.lo -MD -MP -MF .deps/libsimd_avx2_la-core_pmatrix_avx2.Tpo -c core_pmatrix_avx2.c -fPIC -DPIC -o .libs/libsimd_avx2_la-core_pmatrix_avx2.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -mfma -mavx2 -g -MT libsimd_avx2_la-core_pmatrix_avx2.lo -MD -MP -MF .deps/libsimd_avx2_la-core_pmatrix_avx2.Tpo -c core_pmatrix_avx2.c -o libsimd_avx2_la-core_pmatrix_avx2.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -mfma -mavx2 -g -MT libsimd_avx2_la-core_likelihood_avx2.lo -MD -MP -MF .deps/libsimd_avx2_la-core_likelihood_avx2.Tpo -c core_likelihood_avx2.c -fPIC -DPIC -o .libs/libsimd_avx2_la-core_likelihood_avx2.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -mfma -mavx2 -g -MT libsimd_avx2_la-core_likelihood_avx2.lo -MD -MP -MF .deps/libsimd_avx2_la-core_likelihood_avx2.Tpo -c core_likelihood_avx2.c -o libsimd_avx2_la-core_likelihood_avx2.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -mfma -mavx2 -g -MT libsimd_avx2_la-fast_parsimony_avx2.lo -MD -MP -MF .deps/libsimd_avx2_la-fast_parsimony_avx2.Tpo -c fast_parsimony_avx2.c -fPIC -DPIC -o .libs/libsimd_avx2_la-fast_parsimony_avx2.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -mfma -mavx2 -g -MT libsimd_avx2_la-fast_parsimony_avx2.lo -MD -MP -MF .deps/libsimd_avx2_la-fast_parsimony_avx2.Tpo -c fast_parsimony_avx2.c -o libsimd_avx2_la-fast_parsimony_avx2.o >/dev/null 2>&1
libtool: link: ar cru .libs/libsimd_avx2.a .libs/libsimd_avx2_la-core_partials_avx2.o .libs/libsimd_avx2_la-core_derivatives_avx2.o .libs/libsimd_avx2_la-core_pmatrix_avx2.o .libs/libsimd_avx2_la-core_likelihood_avx2.o .libs/libsimd_avx2_la-fast_parsimony_avx2.o
libtool: link: ranlib .libs/libsimd_avx2.a
libtool: link: ( cd ".libs" && rm -f "libsimd_avx2.la" && ln -s "../libsimd_avx2.la" "libsimd_avx2.la" )
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -mavx -g -MT libsimd_avx_la-core_partials_avx.lo -MD -MP -MF .deps/libsimd_avx_la-core_partials_avx.Tpo -c core_partials_avx.c -fPIC -DPIC -o .libs/libsimd_avx_la-core_partials_avx.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -mavx -g -MT libsimd_avx_la-core_partials_avx.lo -MD -MP -MF .deps/libsimd_avx_la-core_partials_avx.Tpo -c core_partials_avx.c -o libsimd_avx_la-core_partials_avx.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -mavx -g -MT libsimd_avx_la-core_derivatives_avx.lo -MD -MP -MF .deps/libsimd_avx_la-core_derivatives_avx.Tpo -c core_derivatives_avx.c -fPIC -DPIC -o .libs/libsimd_avx_la-core_derivatives_avx.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -mavx -g -MT libsimd_avx_la-core_derivatives_avx.lo -MD -MP -MF .deps/libsimd_avx_la-core_derivatives_avx.Tpo -c core_derivatives_avx.c -o libsimd_avx_la-core_derivatives_avx.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -mavx -g -MT libsimd_avx_la-core_pmatrix_avx.lo -MD -MP -MF .deps/libsimd_avx_la-core_pmatrix_avx.Tpo -c core_pmatrix_avx.c -fPIC -DPIC -o .libs/libsimd_avx_la-core_pmatrix_avx.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -mavx -g -MT libsimd_avx_la-core_pmatrix_avx.lo -MD -MP -MF .deps/libsimd_avx_la-core_pmatrix_avx.Tpo -c core_pmatrix_avx.c -o libsimd_avx_la-core_pmatrix_avx.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -mavx -g -MT libsimd_avx_la-core_likelihood_avx.lo -MD -MP -MF .deps/libsimd_avx_la-core_likelihood_avx.Tpo -c core_likelihood_avx.c -fPIC -DPIC -o .libs/libsimd_avx_la-core_likelihood_avx.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -mavx -g -MT libsimd_avx_la-core_likelihood_avx.lo -MD -MP -MF .deps/libsimd_avx_la-core_likelihood_avx.Tpo -c core_likelihood_avx.c -o libsimd_avx_la-core_likelihood_avx.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -mavx -g -MT libsimd_avx_la-fast_parsimony_avx.lo -MD -MP -MF .deps/libsimd_avx_la-fast_parsimony_avx.Tpo -c fast_parsimony_avx.c -fPIC -DPIC -o .libs/libsimd_avx_la-fast_parsimony_avx.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -mavx -g -MT libsimd_avx_la-fast_parsimony_avx.lo -MD -MP -MF .deps/libsimd_avx_la-fast_parsimony_avx.Tpo -c fast_parsimony_avx.c -o libsimd_avx_la-fast_parsimony_avx.o >/dev/null 2>&1
libtool: link: ar cru .libs/libsimd_avx.a .libs/libsimd_avx_la-core_partials_avx.o .libs/libsimd_avx_la-core_derivatives_avx.o .libs/libsimd_avx_la-core_pmatrix_avx.o .libs/libsimd_avx_la-core_likelihood_avx.o .libs/libsimd_avx_la-fast_parsimony_avx.o
libtool: link: ranlib .libs/libsimd_avx.a
libtool: link: ( cd ".libs" && rm -f "libsimd_avx.la" && ln -s "../libsimd_avx.la" "libsimd_avx.la" )
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -msse3 -g -MT libsimd_sse_la-core_partials_sse.lo -MD -MP -MF .deps/libsimd_sse_la-core_partials_sse.Tpo -c core_partials_sse.c -fPIC -DPIC -o .libs/libsimd_sse_la-core_partials_sse.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -msse3 -g -MT libsimd_sse_la-core_partials_sse.lo -MD -MP -MF .deps/libsimd_sse_la-core_partials_sse.Tpo -c core_partials_sse.c -o libsimd_sse_la-core_partials_sse.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -msse3 -g -MT libsimd_sse_la-core_derivatives_sse.lo -MD -MP -MF .deps/libsimd_sse_la-core_derivatives_sse.Tpo -c core_derivatives_sse.c -fPIC -DPIC -o .libs/libsimd_sse_la-core_derivatives_sse.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -msse3 -g -MT libsimd_sse_la-core_derivatives_sse.lo -MD -MP -MF .deps/libsimd_sse_la-core_derivatives_sse.Tpo -c core_derivatives_sse.c -o libsimd_sse_la-core_derivatives_sse.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -msse3 -g -MT libsimd_sse_la-core_likelihood_sse.lo -MD -MP -MF .deps/libsimd_sse_la-core_likelihood_sse.Tpo -c core_likelihood_sse.c -fPIC -DPIC -o .libs/libsimd_sse_la-core_likelihood_sse.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -msse3 -g -MT libsimd_sse_la-core_likelihood_sse.lo -MD -MP -MF .deps/libsimd_sse_la-core_likelihood_sse.Tpo -c core_likelihood_sse.c -o libsimd_sse_la-core_likelihood_sse.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -msse3 -g -MT libsimd_sse_la-core_pmatrix_sse.lo -MD -MP -MF .deps/libsimd_sse_la-core_pmatrix_sse.Tpo -c core_pmatrix_sse.c -fPIC -DPIC -o .libs/libsimd_sse_la-core_pmatrix_sse.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -msse3 -g -MT libsimd_sse_la-core_pmatrix_sse.lo -MD -MP -MF .deps/libsimd_sse_la-core_pmatrix_sse.Tpo -c core_pmatrix_sse.c -o libsimd_sse_la-core_pmatrix_sse.o >/dev/null 2>&1
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -msse3 -g -MT libsimd_sse_la-fast_parsimony_sse.lo -MD -MP -MF .deps/libsimd_sse_la-fast_parsimony_sse.Tpo -c fast_parsimony_sse.c -fPIC -DPIC -o .libs/libsimd_sse_la-fast_parsimony_sse.o
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -Wall -Wsign-compare -D_GNU_SOURCE -std=c99 -O3 -fPIC -msse3 -g -MT libsimd_sse_la-fast_parsimony_sse.lo -MD -MP -MF .deps/libsimd_sse_la-fast_parsimony_sse.Tpo -c fast_parsimony_sse.c -o libsimd_sse_la-fast_parsimony_sse.o >/dev/null 2>&1
libtool: link: ar cru .libs/libsimd_sse.a .libs/libsimd_sse_la-core_partials_sse.o .libs/libsimd_sse_la-core_derivatives_sse.o .libs/libsimd_sse_la-core_likelihood_sse.o .libs/libsimd_sse_la-core_pmatrix_sse.o .libs/libsimd_sse_la-fast_parsimony_sse.o
libtool: link: ranlib .libs/libsimd_sse.a
libtool: link: ( cd ".libs" && rm -f "libsimd_sse.la" && ln -s "../libsimd_sse.la" "libsimd_sse.la" )
libtool: link: gcc -shared -fPIC -DPIC .libs/libpll_la-fasta.o .libs/libpll_la-gamma.o .libs/libpll_la-likelihood.o .libs/libpll_la-list.o .libs/libpll_la-maps.o .libs/libpll_la-models.o .libs/libpll_la-pll.o .libs/libpll_la-output.o .libs/libpll_la-utree.o .libs/libpll_la-rtree.o .libs/libpll_la-derivatives.o .libs/libpll_la-partials.o .libs/libpll_la-compress.o .libs/libpll_la-utree_moves.o .libs/libpll_la-utree_svg.o .libs/libpll_la-parsimony.o .libs/libpll_la-core_derivatives.o .libs/libpll_la-core_partials.o .libs/libpll_la-core_pmatrix.o .libs/libpll_la-core_likelihood.o .libs/libpll_la-parse_utree.o .libs/libpll_la-parse_rtree.o .libs/libpll_la-lex_utree.o .libs/libpll_la-lex_rtree.o .libs/libpll_la-fast_parsimony.o .libs/libpll_la-stepwise.o .libs/libpll_la-random.o .libs/libpll_la-phylip.o .libs/libpll_la-hardware.o .libs/libpll_la-repeats.o -Wl,--whole-archive ./.libs/libsimd_avx2.a ./.libs/libsimd_avx.a ./.libs/libsimd_sse.a -Wl,--no-whole-archive -lm -O3 -Wl,-soname -Wl,libpll.so.0 -o .libs/libpll.so.0.0.0
libtool: link: (cd ".libs" && rm -f "libpll.so.0" && ln -s "libpll.so.0.0.0" "libpll.so.0")
libtool: link: (cd ".libs" && rm -f "libpll.so" && ln -s "libpll.so.0.0.0" "libpll.so")
libtool: link: (cd .libs/libpll.lax/libsimd_avx2.a && ar x "/home/jean-baptiste/modeltest/libs/pll-modules/libs/libpll/src/./.libs/libsimd_avx2.a")
libtool: link: (cd .libs/libpll.lax/libsimd_avx.a && ar x "/home/jean-baptiste/modeltest/libs/pll-modules/libs/libpll/src/./.libs/libsimd_avx.a")
libtool: link: (cd .libs/libpll.lax/libsimd_sse.a && ar x "/home/jean-baptiste/modeltest/libs/pll-modules/libs/libpll/src/./.libs/libsimd_sse.a")
libtool: link: ar cru .libs/libpll.a libpll_la-fasta.o libpll_la-gamma.o libpll_la-likelihood.o libpll_la-list.o libpll_la-maps.o libpll_la-models.o libpll_la-pll.o libpll_la-output.o libpll_la-utree.o libpll_la-rtree.o libpll_la-derivatives.o libpll_la-partials.o libpll_la-compress.o libpll_la-utree_moves.o libpll_la-utree_svg.o libpll_la-parsimony.o libpll_la-core_derivatives.o libpll_la-core_partials.o libpll_la-core_pmatrix.o libpll_la-core_likelihood.o libpll_la-parse_utree.o libpll_la-parse_rtree.o libpll_la-lex_utree.o libpll_la-lex_rtree.o libpll_la-fast_parsimony.o libpll_la-stepwise.o libpll_la-random.o libpll_la-phylip.o libpll_la-hardware.o libpll_la-repeats.o .libs/libpll.lax/libsimd_avx2.a/libsimd_avx2_la-core_derivatives_avx2.o .libs/libpll.lax/libsimd_avx2.a/libsimd_avx2_la-core_likelihood_avx2.o .libs/libpll.lax/libsimd_avx2.a/libsimd_avx2_la-core_partials_avx2.o .libs/libpll.lax/libsimd_avx2.a/libsimd_avx2_la-core_pmatrix_avx2.o .libs/libpll.lax/libsimd_avx2.a/libsimd_avx2_la-fast_parsimony_avx2.o .libs/libpll.lax/libsimd_avx.a/libsimd_avx_la-core_derivatives_avx.o .libs/libpll.lax/libsimd_avx.a/libsimd_avx_la-core_likelihood_avx.o .libs/libpll.lax/libsimd_avx.a/libsimd_avx_la-core_partials_avx.o .libs/libpll.lax/libsimd_avx.a/libsimd_avx_la-core_pmatrix_avx.o .libs/libpll.lax/libsimd_avx.a/libsimd_avx_la-fast_parsimony_avx.o .libs/libpll.lax/libsimd_sse.a/libsimd_sse_la-core_derivatives_sse.o .libs/libpll.lax/libsimd_sse.a/libsimd_sse_la-core_likelihood_sse.o .libs/libpll.lax/libsimd_sse.a/libsimd_sse_la-core_partials_sse.o .libs/libpll.lax/libsimd_sse.a/libsimd_sse_la-core_pmatrix_sse.o .libs/libpll.lax/libsimd_sse.a/libsimd_sse_la-fast_parsimony_sse.o
libtool: link: ranlib .libs/libpll.a
libtool: link: rm -fr .libs/libpll.lax
libtool: link: ( cd ".libs" && rm -f "libpll.la" && ln -s "../libpll.la" "libpll.la" )
/bin/mkdir -p '/home/jean-baptiste/modeltest/build/localdeps/lib'
/bin/bash ../libtool --mode=install /usr/bin/install -c libpll.la '/home/jean-baptiste/modeltest/build/localdeps/lib'
libtool: install: /usr/bin/install -c .libs/libpll.so.0.0.0 /home/jean-baptiste/modeltest/build/localdeps/lib/libpll.so.0.0.0
libtool: install: (cd /home/jean-baptiste/modeltest/build/localdeps/lib && { ln -s -f libpll.so.0.0.0 libpll.so.0 || { rm -f libpll.so.0 && ln -s libpll.so.0.0.0 libpll.so.0; }; })
libtool: install: (cd /home/jean-baptiste/modeltest/build/localdeps/lib && { ln -s -f libpll.so.0.0.0 libpll.so || { rm -f libpll.so && ln -s libpll.so.0.0.0 libpll.so; }; })
libtool: install: /usr/bin/install -c .libs/libpll.lai /home/jean-baptiste/modeltest/build/localdeps/lib/libpll.la
libtool: install: /usr/bin/install -c .libs/libpll.a /home/jean-baptiste/modeltest/build/localdeps/lib/libpll.a
libtool: install: chmod 644 /home/jean-baptiste/modeltest/build/localdeps/lib/libpll.a
libtool: install: ranlib /home/jean-baptiste/modeltest/build/localdeps/lib/libpll.a
libtool: finish: PATH="/home/jean-baptiste/bwa-0.7.3a:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/cd-hit:/usr/lib/cd-hit:/sbin" ldconfig -n /home/jean-baptiste/modeltest/build/localdeps/lib

Libraries have been installed in:
/home/jean-baptiste/modeltest/build/localdeps/lib

If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:

• add LIBDIR to the `LD_LIBRARY_PATH' environment variable
  during execution
• add LIBDIR to the `LD_RUN_PATH' environment variable
  during linking
• use the `-Wl,-rpath -Wl,LIBDIR' linker flag
• have your system administrator add LIBDIR to `/etc/ld.so.conf'

See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.

/bin/mkdir -p '/home/jean-baptiste/modeltest/build/localdeps/include/libpll'
/usr/bin/install -c -m 644 pll.h '/home/jean-baptiste/modeltest/build/localdeps/include/libpll'
Making install in man
/bin/mkdir -p '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll'
/usr/bin/install -c -m 644 libpll_manual.pdf '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll'
/bin/mkdir -p '/home/jean-baptiste/modeltest/build/localdeps/share/man/man3'
/usr/bin/install -c -m 644 libpll.3 '/home/jean-baptiste/modeltest/build/localdeps/share/man/man3'
Making install in examples
/bin/mkdir -p '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/heterotachy'
/usr/bin/install -c -m 644 heterotachy/heterotachy.c heterotachy/Makefile heterotachy/README.md '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/heterotachy'
/bin/mkdir -p '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/lg4'
/usr/bin/install -c -m 644 lg4/lg4.c lg4/Makefile '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/lg4'
/bin/mkdir -p '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/lg4/data'
/usr/bin/install -c -m 644 lg4/data/example.fas lg4/data/example.tree '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/lg4/data'
/bin/mkdir -p '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/load-utree'
/usr/bin/install -c -m 644 load-utree/load-utree.c load-utree/Makefile load-utree/README.md '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/load-utree'
/bin/mkdir -p '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/newick-fasta-rooted'
/usr/bin/install -c -m 644 newick-fasta-rooted/newick-fasta-rooted.c newick-fasta-rooted/Makefile '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/newick-fasta-rooted'
/bin/mkdir -p '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/newick-fasta-unrooted'
/usr/bin/install -c -m 644 newick-fasta-unrooted/newick-fasta-unrooted.c newick-fasta-unrooted/Makefile '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/newick-fasta-unrooted'
/bin/mkdir -p '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/newick-phylip-unrooted'
/usr/bin/install -c -m 644 newick-phylip-unrooted/newick-phylip-unrooted.c newick-phylip-unrooted/Makefile '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/newick-phylip-unrooted'
/bin/mkdir -p '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/newton'
/usr/bin/install -c -m 644 newton/newton.c newton/Makefile newton/README.md '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/newton'
/bin/mkdir -p '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/parsimony'
/usr/bin/install -c -m 644 parsimony/npr-pars.c parsimony/Makefile '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/parsimony'
/bin/mkdir -p '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/partial-traversal'
/usr/bin/install -c -m 644 partial-traversal/partial.c partial-traversal/Makefile '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/partial-traversal'
/bin/mkdir -p '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/protein-list'
/usr/bin/install -c -m 644 protein-list/protein-list.c protein-list/Makefile '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/protein-list'
/bin/mkdir -p '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/rooted'
/usr/bin/install -c -m 644 rooted/rooted.c rooted/Makefile rooted/README.md '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/rooted'
/bin/mkdir -p '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/rooted-tacg'
/usr/bin/install -c -m 644 rooted-tacg/rooted-tacg.c rooted-tacg/Makefile '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/rooted-tacg'
/bin/mkdir -p '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/stepwise'
/usr/bin/install -c -m 644 stepwise/stepwise.c stepwise/Makefile '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/stepwise'
/bin/mkdir -p '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/unrooted'
/usr/bin/install -c -m 644 unrooted/unrooted.c unrooted/Makefile unrooted/README.md '/home/jean-baptiste/modeltest/build/localdeps/share/doc/libpll/examples/unrooted'
aclocal: installing 'm4/libtool.m4' from '/usr/share/aclocal/libtool.m4'
aclocal: installing 'm4/ltoptions.m4' from '/usr/share/aclocal/ltoptions.m4'
aclocal: installing 'm4/ltsugar.m4' from '/usr/share/aclocal/ltsugar.m4'
aclocal: installing 'm4/ltversion.m4' from '/usr/share/aclocal/ltversion.m4'
aclocal: installing 'm4/ltobsolete.m4' from '/usr/share/aclocal/ltobsolete.m4'
libtoolize: putting macros in AC_CONFIG_MACRO_DIR, m4'. libtoolize: copying file m4/libtool.m4'
libtoolize: copying file m4/ltoptions.m4' libtoolize: copying file m4/ltsugar.m4'
libtoolize: copying file m4/ltversion.m4' libtoolize: copying file m4/lt~obsolete.m4'
configure.ac:17: installing '../../compile'
configure.ac:11: installing '../../config.guess'
configure.ac:11: installing '../../config.sub'
configure.ac:18: error: required file '../../ltmain.sh' not found
configure.ac:6: installing '../../missing'
src/algorithm/Makefile.am: installing '../../depcomp'
configure.ac: installing '../../ylwrap'
autoreconf: automake failed with exit status: 1
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 3458764513820540925
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @file support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
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checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
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checking for flex... flex
checking lex output file root... lex.yy
checking lex library... -lfl
checking whether yytext is a pointer... yes
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checking whether C compiler accepts -msse4.2... yes
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checking whether AES is supported by the processor... yes
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checking whether C compiler accepts -maes... yes
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checking whether AVX is supported by the processor and OS... yes
checking whether C compiler accepts -mavx... yes
checking whether FMA3 is supported by the processor... yes
checking whether FMA3 is supported by the processor and OS... yes
checking whether C compiler accepts -mfma... yes
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checking whether XOP is supported by the processor... no
checking whether AVX2 is supported by the processor... yes
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checking whether C compiler accepts -mavx2... yes
checking whether AVX512-F is supported by the processor... no
checking whether AVX512-CD is supported by the processor... no
checking whether AVX512-PF is supported by the processor... no
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checking whether AVX512-VL is supported by the processor... no
checking whether AVX512-BW is supported by the processor... no
checking whether AVX512-DQ is supported by the processor... no
checking whether AVX512-IFMA is supported by the processor... no
checking whether AVX512-VBMI is supported by the processor... no
checking for pll_partition_create in -lpll... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: error: cannot find input file: Makefile.in' make[3]: *** No rule to make target install'. Stop.
make[2]: *** [localdeps/lib/libpll.a] Error 2
make[1]: *** [libs/CMakeFiles/libpll.dir/all] Error 2
make: *** [all] Error 2

Hi,

Have you ever thinking about proposing ModelTest-NG as Conda package?
You can do that by participate to the Bioconda channel

Hi,
did anyone successfully compiled Windows binaries? It would be great to have Windows binaries at least for the command-line version. Thank you,
Tomas

Hi,

I am running modeltest-ng to get the best-fit model for raxml-ng. Out of the 30 genes in my file, one of them was aborted half way in the run and received error "Floating point exception (core dumped)" from modeltest-ng.

Here is the command I was using:
modeltest-ng -d aa -i C0256.laln -o C0256.laln.mt -ff

I saw previous discussion suggested to use only single core for the run (I tried -p 1), but the error still persisted in my case.

I tried a few parameter options on the run and it happened to stop when it is supposed to calculate model+I+G4. As according to the manual, modeltest-ng was considering both the proportion of invariant sites (I) and gamma rate categories (G) in searching the best model with optimum rate heterogeneity by default. So I tested a few times to include I and G option separately in the run. Surprisingly, my file was able to run properly.

However, I would prefer to obtain the best-fit model by including the calculation of both I and G for my sequences or at least understand further on what was happening in the run before opting to either I or G (just in case I have to). Floating point exception sounds something like zero division error to me. Does anybody have any idea on the error and what I should do about it?

Thanks!
Bhei

Installation seems to be failing due to some error related to g++ on a CentOS shared cluster. Not sure what the issue is as compiling from source is not something I am terribly familiar with. It seems that the problem is in the following command:

g++ -g -O3 -Wall -static -static-libstdc++ -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -L/home/XXXXXX/software/modeltest/build/lib -o modeltest-ng genesis/modeltest_ng-date_time.o genesis/modeltest_ng-string.o genesis/modeltest_ng-logging.o modeltest_ng-static_analyzer.o service/modeltest_ng-modeltestservice.o service/modeltest_ng-checkpoint.o thread/modeltest_ng-observer.o thread/modeltest_ng-parallel_context.o model/modeltest_ng-abstract_parameter.o model/modeltest_ng-parameter_branches.o model/modeltest_ng-parameter_ratecats.o model/modeltest_ng-parameter_gamma.o model/modeltest_ng-parameter_pinv.o model/modeltest_ng-parameter_substrates.o model/modeltest_ng-parameter_frequencies.o model/modeltest_ng-model.o model/modeltest_ng-dnamodel.o model/modeltest_ng-protmodel.o optimize/modeltest_ng-model_optimizer_pll.o optimize/modeltest_ng-partition_optimizer.o modeltest_ng-model_selection.o modeltest_ng-modeltest.o modeltest_ng-msapll.o modeltest_ng-partition.o modeltest_ng-partitioning_scheme.o modeltest_ng-treepll.o modeltest_ng-utils.o modeltest_ng-meta.o modeltest_ng-main.o -lpll_binary -lpll_algorithm -lpll_optimize -lpll_msa -lpll_tree -lpll_util -lpll -lm
/usr/bin/ld: cannot find -lpthread
/usr/bin/ld: cannot find -lstdc++
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lc
collect2: error: ld returned 1 exit status
make[2]: *** [modeltest-ng] Error 1
make[2]: Leaving directory /home/XXXXXX/software/modeltest/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory /home/XXXXXX/software/modeltest'
make: *** [all] Error 2

build.log

Hi Diego,

I am testing modeltest-ng on some of my aa alignments in fasta format and so far I always get an "Cannot parse the msa: Wrong sites read" error. For example
$modeltest-ng -d aa -i ../Alignments/OG0010000.fa -T raxml -p 6

produces

modeltest: Cannot parse the msa: ../Alignments/OG0010000.fa
           [10200]: Wrong sites read [Seq 1] 1005 vs 1006
Error: Invalid arguments
Try `modeltest --help` for more information

What may be going wrong here?

Thanks

OG0010000.fa:

>Egrandis_Eucgr.J01883.1
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
-----------------MGVSYRPHPRRPSNLLPCLIALSLFSISALLLYKVDDFASQTK
TVAGHNLDPTPWHLFPPKTFNEKTRYARASKIIQCSYLTCPYA-----TGSIRGQDLSRS
RSA-----RACPAFFAWIRRDLEPWVRTGISPAHLMEAKRFASFRVVIFEGKLYVDFYYA
CVQSRAMFTIWGLLQLLRRYPGMVPDVDLMFDCMDKPSINRTEHASMPLPLFRYCTTPGH
FDIPFPDWSFWGWPETNLKPWDEEFRDIKQGSQVLRWSKKSPYAYWKGNPDVESPVRTEL
LKCNHSRMWNAQVMRQDWAEEARAGYEQSKLSNQCNHRYKIYAEGYAWSVSLKYIIACGS
PALIISPEYEDFFSRGLFPMRNYWPISSTNLCPSIKYAVNWGNANPSEAEAIGKRGQDFM
EDLSMDRIYDYMYHLIMEYSKLQNFKPIPSSSAREVCVDSLLCFADP-KQRQFLERSTAL
ASEEAPCTFKAARGITVTSWIKQKEKAIQDVRKKEMLSAERQ*---
>Athaliana_AT1G07220.1
M-----------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------GLRLR-------------------
-----------------LRLPHKSSPRSPSYLLLCVLALSFFSFTALLFYKVDDFIAQTK
TLAGHNLEPTPWHIFPRKSFSAATKHSQAYRILQCSYFSCPYK-----AVVQPKSLHSES
GSGRQTHQPQCPDFFRWIHRDLEPWAKTGVTKEHVKRAKANAAFRVVILSGKLYVDLYYA
CVQSRMMFTIWGILQLLTKYPGMVPDVDMMFDCMDKPIINQTEYQSFPVPLFRYCTNEAH
LDIPFPDWSFWGWSETNLRPWEEEFGDIKQGSRRRSWYNKQPRAYWKGNPDVVSPIRLEL
MKCNHSRLWGAQIMRQDWAEEAKGGFEQSKLSNQCNHRYKIYAEGYAWSVSLKYILSCGS
MTLIISPEYEDFFSRGLLPKENYWPISPTDLCRSIKYAVDWGNSNPSEAETIGKRGQGYM
ESLSMNRVYDYMFHLITEYSKLQKFKPEKPASANEVCAGSLLCIAEQ-KERELLERSRVV
PSLDQPCKFPVEDRNRLEWLIQQKNKTIENVRYMEMTRTQRGSK--
>Pan_PanWU01x14_asm01_ann01_134260.1
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
-----------------MRLGTRNMRRSPSYLLSCVAALAFLSLTVLVLHKVDDFATQTK
TVVGHNLQPTPWHLFPPKTFSEETRQARVYKILHCSYLACSGY-----TTKSYATERRRS
ASA-DAASQKCPEFFKWIRRDFEPWSRAGISKSHLREAQEFAAFRVVIVGGRLFVDLYYA
CVQSRAMFTIWGLLQLLRRYPGMLPDVDMMFDCMDKPSINQTEHGSMPLPLFRYCTTKAH
FDIPFPDWSFWGWPETNLNPWDEEFRDIKHGSQKMNWTRRWPRAFWKGNPDVGSPVRTEL
LNCNHSRKWGAHILRQDWSKEAKEGYEKSKLSNQCNYRYKIYAEGYAWSVSLKYILSCGS
LALIISPQYEDFFSRGLIPKKNYWPISFSDLCPSIKYAVDWGNAHPSEATAIGKAGQDFM
ASLSMNRVYDYMFHLIKEYSKLQHFKPVRPSSALEVCSESLLCLADE-KQRQLLEKSIAY
PSPSPPCFL*------------------------------------
>Gmax_Glyma.11G174900.1
M--------------CHSTPQ---------------------------------------
---------------------------------PQCT-----------------------
------------------------------------------------------------
------------------------------------------------------------
KTTLF-------------------------------------------------------
----------LLLLL---------------------------------------------
----------------------------------------------------HHSQFFSS
---------------------------------------SS-------------------
----------------NMGPSSTHTPRSPTYLIPCVIALALFSLTGLLLYKVDDVASRTG
TVVGHNLEPTPWHVFPHKPFDEESRQQRAYKILQCSYLTCRYA-----AEALGGARRRT-
----GGGREECPKFFRAIHRDLAPWSESRISKAHVAAAQRYAAFRVVIVEGKVFVDWYYA
CVQSRAMFTLWGLLQLMRRYPGMVPDVDMMFDCMDKPSVNKTEHQAMPLPLFRYCTTKEH
FDIPFPDWSFWGWSEINIRPWQEEFPDIKRGSRSVTWKNKLPWAYWKGNPDVASPIRTEL
INCNDSRKWGAEIMRQDWGEAARNGFKQSKLSDQCNHRYKIYAEGYAWSVSLKYILSCGS
VALIISPQYEDFFSRGLIPNHNFWLVDPLNLCPSIKYAVEWGNQHPVEAEAIGKRGQDLM
ESLNMNRIYEYMFHLISDYSKLQDFKPTPPPTALEVCVESVLCFADE-KQRMFLNKSFTF
PSHKPPCNLKPA*---------------------------------
>Tor_TorRG33x02_asm01_ann01_187660.1
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
-----------------MGLGTRNMPRSPSYLLPCVAALAFLSLTVLVLHKVDDFATQTK
TVVGHNLQPTPWHLFPPKTFSEETRQARVYKILHCSYLACSGY-----TTKSYATERRRS
ASA-DAASQKCPEFFKWIRRDLEPWSRTGISKSHLREAREFAAFRVVIVGGRLFVDLYYA
CVQSRAMFTIWGLLQLLRRYPGMVPDVDIMFDCMDKPSINRTEHGSMPLPLFRYCTTKAH
FDIPFPDWSFWGWPETNLNPWDEEFRDIKHGSQKMNWTRRWPRAFWKGNPDVGSPVRTEL
LNCNHSRKWGAQILRQDWSKEAKEGYEKSKLSNQCNYRYKIYAEGYAWSVSLKYILSCGS
LALIISPQYEDFFSRGLIPKKNYWPISFSDLCPSIKYAVDWGNAHPSEATAIGKGGQDFM
ASLSMNRVYDYMFHLIKEYSKLQHFKPVRPSSALEVCSESLLCLADE-KQRQLLEKSIAH
PSPTPPCFL*------------------------------------
>Ptrichocarpa_Potri.001G252000.1
M-----------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
-AAPL-------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
---------------------------------------SR-------------------
---------------------NKAPARLSSSPLLWIIALA--SLTVFFLYKVDNLALQTK
TVAGHNLPPTPWHLFPPKNFDDQSRHARAYQILHCSYLTCPYS-----NTTVSKGHGFNS
----PSSSPKCPRLFMFIHHDLEPWAQSRITVDHIMGAKNYASFRVVIYKGRLYLDPYYA
CVQSRMMFTIWGFLQLLKRYPGMVPDVDIMFDCMDKPSINKTEHDSFPLPLFRYCTTKDH
FDIPFPDWSFWGWPEVNIRPWDEEFRDIKRGAQARSWPKKWPRAYWKGNPDVGSPTRTSL
LECNHTKKWGAQIMRQDWEEEAKGGYVSSKLSHQCDYRYKIYAEGFAWSVSLKYIISCGS
LALIISPQYEDFFSRGLIPEKNYWPVSSDGLCQSIKFAVDWGNTNPTEAQKIGKAGQDLM
ESLSMDRVYDYMFHLISEYSKLQDFKPVPPSSALEVCVDSLTCFADE-KQKRFFERATAF
PSPSPPCTLQPANSDFIKSWMQQKQRTITNVREMELKA*-------
>Fvesca_Fvesca.gene07900
MEDPETDRNHHESVPSSSSPSTSQTQEQTEQQEQQRRSTSTFSYRVNVLISDVAAFDMKD
DFWSGFIVLVTFWFFASMTMILGFFGSADLQLGPNCSRLIRTNPFFVQTIKLLNVHLTDL
VFKQAQEIEGTKPGSILYGFYIPPPLDDEIAWTETHHTLEWIYFLNKGSRIDIYYHVKPS
SSSPLTLVIAQGRESLVEWIEDPSYGSGKIHQVISESSSYYIAVGNLNPEDVEADLEFNI
KSTLYNTSQAYYRCSIHNQYCGLELSLLGTTSAVLTSPGPKEGIQEDDWYVKVSYGPRWL
IYFLGSGVMTVLLLMAFRFCSIFQNAGEDRTDFQGREASPVRTPLLLPKDDDALSWGSSY
ECISNDEEDFEEFLGVSSLEGKSINGGDDNNTLRLCVICFDGPRDCFFLPCGHCATCFTC
GTRISEEAGTCPICRMKMKKGPKAVYLESNRKSEISGIQSRIMSYRIPTRVAHLCGPPNA
ATNSITFFFIFIIFIIVMGTLPRTTSRTPSYILRSVIALSCLSL-LFIIYKVNDFASQTK
TVAGHNLDPTPWHPFRPKTFNHDALPSRAYKLLQCSYLACRYTNNKGNATTLEDEDHRRS
ATS-VAKSPQCPEVFRWIHQDLEPWATTKITPVHIEQAKRYAAFRVVIYKGKLYVDLYYA
CVQSRAMFTIWGLLQMLKRYPGRVPDVDFMFDCMDKPTIERSEHASMPLPLFRYCTNDAH
YDIPFPDWSFWGWPETNIEPWDEQFQAIKRGGQETTWRKKELLAYWKGNPDVGSPVRKEL
LNCNDSKTYRAQILKQDWDEEAKAGFQQSSLSKQCNHRYKIYAEGYAWSVSLKYILSCGS
LALVITPQYEDFFSRGLFPKVNYWPISANAICPSIKSAVDWGHGHVPEAQAIGRRGQEYM
ENLNMDRVYDYMFHLITEYSKLQNFKPVPPNTAMEVCANSVLCLADDAKQREYLERTRAK
PFPGPPCDLQPPDGNLINKWKKEKAAVFQTVEDMNLVNDIPEPVP*
>Mtruncatula_Medtr3g464000.1
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
-----------------MAHSSKHTPRTPTYLLPCVIALSFFSLTALLLYKVDDVASRTG
TVVGHNLEPTPWHVFPTKSFDEETRQSRAYKIIQCSYLTCGSADS---GGKTGPSFAAK-
----DAKQQNCPDFFRAIRKDLEPWKKTKISKGHLVEAQKYAAFRVVIVGGKLFVDWYYA
CVQSRAMFTVWSLLQLLRRYPGLVPDVDLMFDCMDKPSINKTEHASMPLPLFRYCTTKGH
FDIPFPDWSFWGWPEINIRPWQEEFPDIKQGAQVVSWKNKNPLAYWKGNPDVASPLRTEL
LTCNDSMKWGAEIMRQDWDAAARSGFQESKLSKQCNHRYKIYAEGYAWSVSLKYILSCGS
VALIIRPQYEDFFTRGLVPLQNFLPVDPLDLCPSIKRNVDWGNKHPKEAAALGKRGQDYM
ESLNIDRIYDYMFHLISEYSKLLDFKPALPSTALVVCEESVLCFADE-KQRSFLSRSTVS
PSQTPPCTLKPA*---------------------------------
>Gmax_Glyma.18G062600.1
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
-----------------MGPSSKHTPRSPTYLIPCVIALALFSLTGLLLYKVDDVASRTG
TVVGHNLEPTPWHVFPHKPFDEESRQQRTYKILQCSYLTCRYA-----AGAVGGSRRSF-
----AGGREECPEFFRAIHRDLAPWLESRISKAHVAAAQRYAAFRVVIVEGKVFVDWYYA
CVQSRAMFTLWGLLQLMRRYPGKVPDVDMMFDCMDKPSVNRTEHQAMPLPLFRYCTTKEH
FDIPFPDWSFWGWSEINIRPWQEEFPDIKQGSRNVSWKNKFPWAYWKGNPDVASPIRTEL
INCNDSRKWGAEIMRQDWGEAARSGFKQSKLSNQCNHRYKIYAEGYAWSVSLKYILSCGS
VALIISPQYEDFFSRGLIPNHNFWLVDSLNLCPSIKYAVEWGNQHPVEAEAIGKRGQDFM
GSLNMDRIYEYMFHLISEYSKLQDFKPTPPTTALEVCVESVLCFADE-KQRMFLNKSTAF
PSHKPPCNLKPA*---------------------------------

Hi, I've got a problem running modeltest-ng:

modeltest-ng: Cannot parse the msa: /home/shadowstep/UNIX/Seq/matK_trim.phylip
              [910]: Sequence 1 (Acorus) longer than expected
Error: Invalid arguments

How can I fix this? Thanks!

Hello,
a client of ours could not run the ModelTest binary on his new MacBook with the new M1 chip architecture.
The error thrown was "Error trying to run modeltest-ng, exited with code 'SIGILL'."
I do not have access to the hardware to examine more, but maybe the code is not compiled correctly for the new chips.

Cmake files are attached.
CMakeError.log
CMakeOutput.log

Hi!
I was having issues installing modeltest-ng, the only thing that finally worked was to download the "modeltest-ng-0.1.5.tar.gz" file, run the "install-with-libpll.sh" script, and then running the "build.sh" script. This resulted in the following:

Running install script for Linux
QMake version 3.1
Using Qt version 5.9.6 in /home/lara/miniconda3/lib
...configuration:
prefix: /home/lara/Downloads/modeltest-ng-0.1.5/build
build: /home/lara/Downloads/modeltest-ng-0.1.5/build
pll: [yes] /home/lara/Downloads/modeltest-ng-0.1.5/libs/pll-modules/libs/libpll
modules: [yes] /home/lara/Downloads/modeltest-ng-0.1.5/libs/pll-modules
include: /home/lara/Downloads/modeltest-ng-0.1.5/build/include
lib: /home/lara/Downloads/modeltest-ng-0.1.5/build/lib

...writing log to /home/lara/Downloads/modeltest-ng-0.1.5/build.log
...build pll
...building pll
...pll OK!
/home/lara/Downloads/modeltest-ng-0.1.5
...build modules
...building modules
...modules OK!
/home/lara/Downloads/modeltest-ng-0.1.5
...build modeltest
...modeltest OK!
...build modeltest GUI
...modeltest GUI FAIL!

This seems to be insufficient because calling "modeltest" results in:
modeltest−ng: command not found

I would also like to use the GUI, can you please advise? Thank you!

I have no idea why the error always happens, please help me. The running log is shown below:
Physical cores: 72
Logical cores: 144
Memory: 1.01e+03GB
Extensions: AVX

WARNING: MSA has not enough sites to infer reliable results
Creating new checkpoint file: Roary.modeltest_aa.ckp

ModelTest-NG vx.y.z

Input data:
MSA: Roary.core.protein.fasta.gb
Tree: Maximum likelihood
file: -
#taxa: 68
#sites: 408785
#patterns: 28829
Max. thread mem: 616 MB

Output:
Log: Roary.modeltest_aa.log
Starting tree: Roary.modeltest_aa.tree
Results: Roary.modeltest_aa.out

Selection options:

protein matrices: 19

protein models: 152

include model parameters:
Uniform: true
p-inv (+I): true
gamma (+G): true
both (+I+G): true
free rates (+R): false
fixed freqs: true
estimated freqs: false
#categories: 4
gamma rates mode: mean
asc bias: none
epsilon (opt): 0.01
epsilon (par): 0.05
keep branches: false

Additional options:
verbosity: very low
threads: 25/72
RNG seed: 12345
subtree repeats: enabled

modeltest was called as follows:

modeltest-ng -i Roary.core.protein.fasta.gb -t ml -o Roary.modeltest_aa -p 25 -d aa

Partition 1/1

24/152 WAG+G4+F 3h:55:25 3h:56:00 -2074729.4442 0.0217 -
16/152 STMTREV+I+G4+F 3h:55:29 3h:56:04 -2033708.7978 0.3549 0.8028
7/152 MTREV+I+G4+F 4h:00:55 4h:01:30 -2025846.5708 0.3549 0.8028
19/152 HIVB+I+G4+F 4h:27:24 4h:27:59 -2014905.1744 0.3549 0.8028
25/152 FLU+G4+F 4h:29:57 4h:30:32 -2075228.6745 0.0834 -
2/152 BLOSUM62+I+G4+F5h:10:07 5h:10:42 -2044177.9120 0.3549 0.8028
20/152 PMB+I+G4+F 5h:11:03 5h:11:38 -2042465.2451 0.3549 0.8028
13/152 MTART+I+G4+F 5h:40:35 5h:41:10 -2050105.3186 0.3194 0.8028
22/152 LG+G4+F 5h:52:19 5h:52:54 -2075627.2338 0.0432 -
21/152 HIVB+G4+F 5h:58:39 5h:59:14 -2073488.2801 0.0742 -
3/152 DAYHOFF+I+G4+F 6h:03:26 6h:04:01 -2021315.0281 0.3860 0.8028
18/152 JTT-DCMUT+I+G4+F6h:06:14 6h:06:49 -2009104.3813 0.3549 0.8028
Error: 0.00000 vs -2183213.80553 [0]
Error: 0.00000 vs -2183213.80553 [0]
Error: 0.00000 vs -2183213.80553 [0]
Error: 0.00000 vs -2183213.80553 [0]
5/152 DCMUT+I+G4+F 6h:29:15 6h:29:50 -2021275.3169 0.3859 0.8028
14/152 MTZOA+I+G4+F 6h:39:37 6h:40:12 -2028414.8689 0.3549 0.8028
12/152 MTMAM+I+G4+F 6h:57:11 6h:57:46 -2040743.0044 0.3343 0.8028
10/152 CPREV+I+G4+F 6h:57:33 6h:58:08 -2021137.9856 0.3855 0.8028
8/152 WAG+I+G4+F 6h:58:20 6h:58:55 -2020229.8723 0.3549 0.8028
29/152 DAYHOFF+G4+F 3h:33:31 7h:35:01 -2075187.3374 0.0416 -
28/152 HIVW+G4+F 3h:44:51 7h:40:55 -2097330.8131 0.0596 -
9/152 RTREV+I+G4+F 7h:42:58 7h:43:33 -2028641.9863 0.3549 0.8028
23/152 STMTREV+G4+F 7h:54:14 7h:54:49 -2089505.1153 0.0218 -
4/152 LG+I+G4+F 7h:54:36 7h:55:11 -2020285.1932 0.3549 0.8028
6/152 JTT+I+G4+F 7h:58:19 7h:58:54 -2008845.3845 0.3549 0.8028
30/152 BLOSUM62+G4+F 4h:30:15 8h:58:14 -2099069.7639 0.0216 -
15/152 HIVW+I+G4+F 9h:16:41 9h:17:16 -2037178.7370 0.3549 0.8028
37/152 DCMUT+G4+F 3h:28:25 9h:32:26 -2075370.0225 0.0390 -
27/152 MTREV+G4+F 5h:39:43 9h:35:43 -2081131.5080 0.0974 -
11/152 VT+I+G4+F 9h:37:32 9h:38:07 -2025429.3813 0.3549 0.8028
38/152 MTMAM+G4+F 3h:42:21 9h:49:10 -2103881.5031 0.1016 -
26/152 JTT-DCMUT+G4+F 10h:05:45 10h:06:20 -2062936.2555 0.0218 -
39/152 RTREV+G4+F 3h:40:17 10h:10:07 -2084702.2863 0.0661 -
34/152 MTZOA+G4+F 4h:44:18 10h:25:28 -2086022.5855 0.1004 -
40/152 MTMAM+I+G4 4h:45:54 11h:26:06 -2125255.6269 0.3158 0.8028
46/152 MTREV+I+G4 4h:18:37 12h:02:10 -2108167.8398 0.3549 0.8028
59/152 DAYHOFF+I+F 0h:37:30 12h:03:36 -2059621.0632 - 0.8429
36/152 MTART+G4+F 6h:12:46 12h:12:00 -2112523.1300 0.0997 -
17/152 FLU+I+G4+F 12h:28:09 12h:28:44 -2016934.0297 0.3549 0.8028
31/152 CPREV+G4+F 8h:07:45 12h:38:17 -2075768.5012 0.0674 -
61/152 FLU+I+F 0h:57:00 13h:00:36 -2059859.0709 - 0.8429
49/152 JTT+I+G4 5h:26:34 13h:25:28 -2014946.1124 0.3549 0.8028
60/152 STMTREV+I+F 1h:33:32 13h:35:42 -2073047.0283 - 0.8429
65/152 PMB+I+F 0h:59:45 14h:00:21 -2080242.4891 - 0.8429
45/152 BLOSUM62+I+G4 6h:26:01 14h:06:56 -2051883.3805 0.3549 0.8028
41/152 CPREV+I+G4 7h:10:25 14h:08:11 -2032771.3711 0.3549 0.8028
48/152 MTZOA+I+G4 6h:27:24 14h:22:35 -2095854.7733 0.3371 0.8028
67/152 MTREV+I+F 0h:47:03 14h:22:45 -2067985.4824 - 0.8429
62/152 JTT-DCMUT+I+F 2h:17:42 14h:29:42 -2046852.9698 - 0.8429
56/152 STMTREV+I+G4 4h:39:26 14h:45:46 -2085176.1499 0.3549 0.8028
Error: 0.00000 vs -2186276.29847 [0]
Error: 0.00000 vs -2186276.29847 [0]
Error: 0.00000 vs -2186276.29847 [0]
Error: 0.00000 vs -2186276.29847 [0]
Error: 0.00000 vs -2186276.29847 [0]
64/152 HIVB+I+F 2h:12:27 14h:50:44 -2056842.3156 - 0.8429
69/152 RTREV+I+F 0h:54:30 15h:01:26 -2068447.7921 - 0.8429
47/152 MTART+I+G4 7h:09:38 15h:04:27 -2136626.3406 0.3589 0.8429
68/152 WAG+I+F 1h:05:25 15h:05:46 -2058135.6022 - 0.8429
53/152 DCMUT+I+G4 5h:30:33 15h:06:16 -2039527.2935 0.3943 0.8028
63/152 HIVW+I+F 2h:37:34 15h:06:18 -2080228.1968 - 0.8429
35/152 JTT+G4+F 9h:23:57 15h:16:51 -2062600.1435 0.0218 -
52/152 HIVW+I+G4 5h:49:07 15h:21:33 -2094483.4966 0.3549 0.8028
42/152 RTREV+I+G4 8h:29:09 15h:27:17 -2050096.1738 0.3549 0.8028
73/152 BLOSUM62+I+F 0h:58:25 15h:28:07 -2082109.8056 - 0.8429
66/152 VT+I+F 2h:15:55 15h:41:23 -2062398.3179 - 0.8429
74/152 MTMAM+I+F 0h:57:46 15h:43:32 -2097342.1863 - 0.8429
72/152 DCMUT+I+F 1h:34:53 15h:57:38 -2059278.5032 - 0.8429
77/152 MTZOA+I+F 1h:02:14 16h:06:41 -2073035.8061 - 0.8429
70/152 CPREV+I+F 2h:09:46 16h:17:57 -2059727.7496 - 0.8429
75/152 MTART+I+F 1h:34:06 16h:24:50 -2103808.3063 - 0.8429
76/152 LG+I+F 1h:30:58 16h:32:24 -2059163.2491 - 0.8429
43/152 VT+I+G4 9h:34:29 16h:33:24 -2031521.6531 0.3549 0.8028
51/152 HIVB+I+G4 7h:19:08 16h:36:24 -2032726.0664 0.3549 0.8028
71/152 JTT+I+F 2h:18:21 16h:40:56 -2046640.0408 - 0.8429
55/152 FLU+I+G4 7h:15:30 17h:04:40 -2051437.7445 0.3549 0.8028
50/152 PMB+I+G4 8h:42:25 17h:40:39 -2050584.5141 0.3549 0.8028
57/152 LG+I+G4 7h:49:27 17h:59:34 -2027135.0768 0.3549 0.8028
97/152 STMTREV+F 0h:20:44 18h:20:18 -2208571.5638 - -
98/152 DAYHOFF+F 0h:14:59 18h:35:17 -2193551.6487 - -
58/152 DAYHOFF+I+G4 8h:10:16 18h:35:44 -2039335.8079 0.3943 0.8028
82/152 FLU+G4 3h:42:24 19h:03:57 -2108720.3159 0.0753 -
44/152 WAG+I+G4 11h:32:18 19h:07:19 -2027842.3988 0.3549 0.8028
100/152 JTT-DCMUT+F 0h:36:57 19h:12:41 -2179852.1666 - -
99/152 FLU+F 0h:41:28 19h:16:45 -2199254.8389 - -
54/152 JTT-DCMUT+I+G4 9h:43:13 19h:21:20 -2015372.3528 0.3549 0.8028
102/152 HIVB+F 0h:24:12 19h:31:31 -2198889.3210 - -
modeltest-ng: /opt/conda/conda-bld/modeltest-ng_1572470208140/work/src/model/parameter_branches.cpp:138: virtual double modeltest::ParameterBranches::optimize(modeltest::mt_opt_params_t*, double, double, bool): Assertion `fabs(cur_loglh - loglh) < 1e-6' failed.

Decide how to display partitioning results in the GUI

Dear Modeltest tead,

Thanks a lot for your Modeltest program!
Sorry, I am trying to create manual.pdf using make (in 'manual/' subdir).
When executed I get the an error.
This is what I am doing:
$ make

OUTPUT
<...truncated...>

Output written on manual.pdf (16 pages, 388829 bytes).
Transcript written on manual.log.
bibtex manual
This is BibTeX, Version 0.99d (TeX Live 2013/Debian)
The top-level auxiliary file: manual.aux
A level-1 auxiliary file: sec-quickstart.aux
A level-1 auxiliary file: sec-arguments.aux
I couldn't open style file natbib.bst
---line 32 of file manual.aux
: \bibstyle{natbib
: }
I'm skipping whatever remains of this command
I found no style file---while reading file manual.aux
(There were 2 error messages)

I think the problem is that I have sty file, but no bst file.
$ kpsewhich natbib.sty
/home/alessandro/texmf/tex/latex/natbib/natbib.sty

$ kpsewhich natbib.bst

Can any one help on this?
Thank you very much in advance,
Alessandro

Allocate memory for partitions sequentially

Hi Diego,

when running
./modeltest-ng -i ENSGT00760000118962.fa -t mp

I get a segfault

#3  0x00000000005c399e in __assert_fail ()
#4  0x00000000004b08f2 in build_tips_recurse (tree=0x2a64c40, tip_labels=0x1e26020, split_len=6) at consensus.c:927
#5  0x00000000004b0662 in build_tips_recurse (split_len=6, tip_labels=0x1e26020, tree=0x1fb39a0) at consensus.c:946
#6  build_tips_recurse (split_len=6, tip_labels=0x1e26020, tree=0x1fb2fe0) at consensus.c:946

You can find the fasta file at https://github.com/BenoitMorel/phd_experiments/blob/master/datasets/bugs/modeltest/ENSGT00760000118962.fa

I reproduced the issue when building from the most recent sources, but also with the last binary release.

Benoit

Discuss how to set arguments for equal/ML (DNA) model/empirical (AA). ModelTest is intended to provide flexibility for including only one set of frequencies, or both.

ProtTest and old ModelTest versions include the equal(DNA)/model(AA) frequencies by default. ML(DNA)/empirical(AA) are included when the argument -F is specified. However, the new version of modeltest uses an argument such as -F [e|m]. For example:

-F e
-F m
-F em

'e' can stand for equal/empirical and 'm' for ML/model. The problem is that one could mix up both, because 'e' increases the number of parameters for protein models, while 'm' does the same for DNA models. If only one single data type is used, this might not be a big deal. However, if the input is a partitioned data set including both DNA and protein data, the user won't be able to choose only those models with or without free parameters on the frequencies.

Other proposal is to use, for example, 'f' and 'e' standing for 'fixed' and 'estimated', instead of 'e' and 'm'. Therefore, 'f' will be used for equal(DNA)/model(AA); and 'e' for ML(DNA)/empirical(AA):

-F f
-F e
-F fe