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```
What steps will reproduce the problem?
1. 20 species (is this too many?) 3 mit genes and 2 nuc genes unliked
models all with gtr estimate freq and gamma+i none are partitioned by
codon. Only one i…
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At present gene trees are only parsed in newick format. Parse in nhx format to preserve information on duplications etc.
A few packages do this, including ggtree: https://bioconductor.org/packages/re…
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Hi all!
I'm using ReRconverge again with the Hiller et al 12 mam dataset (17,598 gene trees, max 82, MT BL estimates from 9712 genes)
but... when I go to estimate the RERs with getallresiduals…
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OrthoFinder version 2.5.4 Copyright (C) 2014 David Emms
2022-04-07 09:18:23 : Starting OrthoFinder 2.5.4
24 thread(s) for highly parallel tasks (BLAST searches etc.)
1 thread(s) for OrthoFinder a…
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I would like to request that all gene family trees be calculated with bootstrap support. This enables downstream users to assess how much to believe tree branches in some circumstances.
Calculatin…
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I ran orthofinder with -msa in hopes that it would add support values to gene trees. And it kind of has. In that some trees have them and some don't. As an example, here are two trees from the same ru…
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Hi ~
I want use Phybase to simulate gene trees (Species tree constructed by Astral), and some articles said it should phased all the terminal tips with a branch length equal to 1. Is there necessary…
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Hello,
Iam trying to run bootstrap analyses with astral on a large dataset (~14000 loci). Unfortunatly the run failed with error message from java which seems related to memory issue?
**To Reprodu…
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Yes, this can be done via the gene search page, but if a user is focused on gene families, it may not be obvious to go use the gene search page instead.
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Hi
Thanks for this great tool. I have used OrthoFinder lots in the past.
I have installed STAG-1.0.0 from the releases page
And when I run the test dataset, I get an invalid syntax error?
…