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Hi, I'm having a problem running orthofinder, it seems to quit after starting to calculating gene distances without giving the normal output. I'm certain all programs are installed and running correct…
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Hello David,
I was wondering if I could get each pruned alignment file that generated when creating the supermatrix. I looked at all of the resulting files, but none of them. I know that I can ge…
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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'm running OrthoFinder 2.2.7 on about 400 bacterial genomes. It has been working well, but the final step (starting with a species tree and orthogroups using the -fg and -s option) only gets through …
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use cd-hit to find duplicate protein substrings in the input protein files
use this for "best" filtering option
needs these files:
cd-hit cdhit.c++ cdhit-common.h cdhit-common.o cdhit.o cd…
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I imagine TSV feature name orthogroup name.
Need to make a list of software outputs (IE ORTHOMCL) and see if there are standard formats to support.
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Is there any outfiles that would be handy to choose one orthologous sequences per species per orthogroup ?
It is to make phylogenies with them.
I could choose the longest but I fear that the longest…
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2021-03-13 16:16:44 : Written final scores for species 117 to graph file
2021-03-13 16:16:45 : Written final scores for species 110 to graph file
2021-03-13 16:16:45 : Written final scores fo…
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Make a "quick start" section in the main README file and move demonstrations of more complicated analyses to a GitHub wiki.
Example of a more complicated analysis to explain in the wiki: creating …
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Hello,
I recently read your article: Convergent and complementary selection shaped gains and losses of eusociality in sweat bees. I am using the selection_pipeline.py script to run the command: pyt…