tbrown91 / simbac Goto Github PK

Hello tbrown91,

I am interested in simulating whole bacterial genomes with your tool to perform alignments. But in order to analyse them, I need the log files generated by the parameters -b and -f.

I tried the commands in the supplementary information. All works fine except from the exemple 2 and I get a core dumped error each time I tried to apply the -b (along with -R and -D ) and the - f (along with -r and -e).
Also, I get an error message saying that the /root is a denied access.

Do you know where those errors may come from?

Thanks,

Samaln

Greetings,

I have an analysis where I'd like to discover regions of selective sweeps in a bacterial genome using some sliding window softwares.

I have multiple groupings of bacterial alignments and want to find significant sites of selective sweep events. I want to use SimBac to create alignments that have mutations that occur randomly along the length of a genome that is equivalent for my bacteria's genome length, and compute a selective sweep value for these simulated alignments. This should provide a null distribution to compare against my experimental data.

Since I have multiple alignments, the mutation rate for each one might be different given varying sizes. I was wondering if you knew of a tool that could look at my alignments and generate statistics like mutation rate?

Hello,

Is there some way to track in which branch of the tree/lineage a given recombination break (given in -b or -f output files) occurs?

I ask because I am specifically interested in identifying simulated recombination events using a tool such as ClonalFrameML, which outputs identified recombinant regions, but the -b and -f options seem to only output START and END locations of the breaks...but not which lineages/leaves they are found in.

Any help is greatly appreciated.

Thank you,
Conrad Izydorczyk

Thanks for the great tool. I need to have the ancestral sequence (reference) as well. Is it possible to get the ancestral sequence for the simulations?

Dear Madam, Dear sir,

I'm having trouble running the program ...

sudo apt-get install gsl-bin libgsl0-dev libgsl0ldbl
Reading package lists... Done
Building dependency tree
Reading state information... Done
Note, selecting 'libgsl-dev' instead of 'libgsl0-dev'
Package libgsl0ldbl is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source
However the following packages replace it:
libgsl23 libgslcblas0:i386 libgsl23:i386 libgslcblas0

E: Package 'libgsl0ldbl' has no installation candidate

SimBac
SimBac: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory

I'm running Linux Mint 19.2 Tina ( base: Ubuntu 18.04 bionic )

Would you happen to have a solution ?

Thanks,
Damien