Handle near-zero branch lengths? about raxml-ng HOT 6 CLOSED

Hi,
I am fitting trees to unpartitioned alignments with little diversity. I'm wondering if you could advise about the best approach for fitting and interpreting branch lengths. Currently, I fit trees using a JC model and correcting for invariant sites.

raxml-ng --all --msa ${fasta} --model ${model}+ASC_STAM{$A_invar/$C_invar/$G_invar/$T_invar}+FU{$a/$c/$g/$t} --prefix ${prefix} --blopt nr_safe --threads $threads
-If my alignment is not partitioned, do I need to do a subsequent step following the model fitting and bootstrapping to optimize branch lengths?
-Should I change the --brlmin parameter to lower than 1e-6 or, instead, after I fit trees, could I set branch lengths inferred to be this minimum 1e-6 length to 0, so that I can visualize where polytomies exist in the fit trees?

Thanks in advance for your help!
Best,

from raxml-ng.

@ksw9 could you please re-post your question in our user support google group:
https://groups.google.com/forum/#!forum/raxml

thanks!

from raxml-ng.

Of course, thanks!

from raxml-ng.

@is there any good model for traits, thanks.

from raxml-ng.

@stamatak @amkozlov I am very interesting about using ml method to do traits phylogenetic, is there any good methods for this?

from raxml-ng.

implemented as of raxml-ng 1.0

from raxml-ng.