Handle near-zero branch lengths?

[stamatak]

This was a recurrent issue in RAxML when dataset had so little diversity that the br-len optimization hit the branch length minimum set in the code. Also need to be careful to maybe resolve inner nodes with zero branch lengths into multi-furcations. There were 1-2 papers discussing this.

[ksw9]

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,

[amkozlov]

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

thanks!

[ksw9]

Of course, thanks!

[ghost]

@is there any good model for traits, thanks.

[ghost]

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

[amkozlov]

implemented as of raxml-ng 1.0