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amkozlov / raxml-ng

RAxML Next Generation: faster, easier-to-use and more flexible
GNU Affero General Public License v3.0
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Handle near-zero branch lengths? #23

Closed stamatak closed 4 years ago

stamatak commented 7 years ago

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 commented 5 years ago

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 commented 5 years ago

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

thanks!

ksw9 commented 5 years ago

Of course, thanks!

ghost commented 5 years ago

@is there any good model for traits, thanks.

ghost commented 5 years ago

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

amkozlov commented 4 years ago

implemented as of raxml-ng 1.0