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Hi! First first of all, thanks for the quite unique piece of software!
In the README it is stated that the `input trees can have missing taxa` with respect to the backbone species tree. However, wi…
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Hi,
I'm running some preliminary analyses using MEME on a set of genes for 4 species. I've encountered a subset of 19 genes in my total dataset (a few thousand genes) that result in a segfault whe…
a-lud updated
3 years ago
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Hi Brant,
I am trying to run phyluce_genetrees_run_raxml_genetrees so that I can generate gene trees for ASTRAL, but it is giving an error after it does uce-2012 each time
phyluce_genetrees_run…
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Hello all,
I have successfully run panX analyses on three different individual genera using,
`./panX.py -fn data/myGenus -sl myGenus -t 2`
I tried to run all three genera together with a total…
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Original question: I followed OrthoFinder Tutorials step by step. Everything is OK, till I go to the last step (2. Running an example OrthoFinder analysis step 8. Run OrthoFinder). When I put 'orthof…
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Talking about this with @andrewkern and @vsbuffalo. Currently, the "Chromosomal inversion" recipe of section 14.4 has a recombination callback that looks like this:
```
recombination() {
if (gen…
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Hello,
I am running into an issue trying to run the pairwise ratio comparisons for a list of alignments. I want to determine if there is support for different dN/dS ratios between genes (i.e. like…
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Hi,
Does ASTRAL accept multi-copy gene trees as input? I raise this question because single-copy genes are restricted in some datasets, especially in plants.
Bests,
Tao
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Hi there! I'm having some sad luck with a big Orthofinder run. This is my first GitHub issue, so I apologize in advance if I share unhelpful info and miss all the actual helpful stuff. I'm happy to sa…
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Hi,
Thanks for the implementation of the Leiden algorithm in your package, I think results are better now, although I still might have some concerns about the resolution parameter, and from some test…