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The docstring for 3.2-run_IgPhyML.py says that `-v` is the "assigned germline V gene of known antibodes, for use in rooting the trees," but I'm running into some instance where it doesn't use this seq…
ressy updated
3 years ago
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Thanks for writing this software. I'm analyzing a large number of alignments that contain as many as a few hundred species. The FASTA header for each sequence in the dataset is unique, containing info…
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HI,
I just notice HGTector has come to the version2
and I install and run successfully.
But I have a question that could it give the source of the HGT?
I mean those genes may come from some certa…
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protein level clustering with MMSeqs2 (faster) and/or OrthoFinder (more traditional)
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Hello,
I am running the pipeline on 9 archaea genomes (4 focal and 5 from NCBI). I have ran up to step 7. It does not fail, in fact it claims it has completed, but it runs pretty much instantly and …
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Hi developer,
I met the error below. How could I deal with it? Besides, for arguments **-d**, after first time I ran the command, the database file **phylophlan.dmnd** was produced. Could I just spec…
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Is there some requirements for the input tree?
FIRST:
Is it important to use whole-genome alignment or is core genome alignment also suitable for tree generation?
SECOND:
What tree would be best to…
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It's now trivial to add a `tskit.Tree.generate_random()` method for generating random bifurcating trees with equal probability for each topology. All we have to do is:
```
def generate_random(self…
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Hello,
I've been having some trouble with Orthofinder 2.4.0 lately. When I attempt to run orthofinder, it seems that I am getting multiple errors in the "Analyzing Orthogroups" section. I've looked t…
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Hello Florent, sorry I think I might have stumbled into another issue in step 08. This time the issue seems to be the GO term analysis, here's the stdout I get:
```This is Pantagruel pipeline versio…