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Dear David,
Orthofinder is such a key part of my work. I am really happy about this brilliant piece of software. I've recently run orthofinder with 8 *.faa sets and 8 *cds.fa sets (all downloaded f…
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Hi,
I successfully run orthofinder using the protein sequences, but I get an error when I run it again using the nucleotide sequences from the same species.
I have DNA sequences for 71 species. Th…
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Greetings I'm a PhD student, working on visualization of synteny across genomes of strains of the same species (12 different synteny plots), and one synteny across different species genomes (up to 35 …
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Hello,
I have 5 .pep files that I'd like to run through Orthofinder. One of them is a reference file I got from NCBI, while the other 4 I generated using TransDecoder (LongOrfs and Predict). This wo…
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Hi,
I've been trying to run a couple datasets (one small and one large) using -M msa + RaxML.
I'm puzzled as to what is happening. I am running the two simultaneously but on different partitio…
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Hi, I still need to go through the details. I just installed and started the Test run. We have sequenced and assembled some ciliate genomes that have never been reported. I am a newbie in the field of…
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Hello,
Apologies if this issue was raised before, I couldn't find it after a search through existing issues.
Since I am very interested in the number of genes per species and orthogroup I have b…
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Hi,
I want to run OrthoFinder from the Gene Trees step onwards. The reason is that I am only interested in the duplication history of a subset of orthogroups. However the default of OrthoFinder is …
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Hi,
I am going to be using CSUBST in an exploratory manner on a number of genes from a phylogeny and I have both a species tree and gene trees (for each gene) available to me. Can you recommend the…
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Hello. This is Woo Jun Bang, and I'm trying to use this program for building orthograph reference data set!
I got this error when I wrote 'sh ortho_dl.sh culicidae 7157 0.9 0.9' for test.
Then I…