davidemms / OrthoFinder

Phylogenetic orthology inference for comparative genomics

https://davidemms.github.io/

davidemms/OrthoFinder Issues

HIV teste 1
Updated 15 days ago
issue with running Orthofinder
Updated 21 days ago2
not an issue, clarification wanted for which sequences are represented in orthogroups
Closed 24 days ago4
Question_process_Orthofinder
Updated 24 days ago1
what is the Orthogroup column in N*.tsv?
Updated 24 days ago1
Single copy orthologs (SCO) are not being generated
Updated a month ago
Species tree make_ultrameric.py not working
Updated a month ago1
[Feature Request] Allow for passing options to Diamond and other dependencies
Updated a month ago
[Possible Bug] The `-og` option doesn't stop after inferring orthogroups
Updated a month ago
total identical sequences clustered into one orthogroup, but the topology of gene tree divided into multiple clades
Updated 2 months ago
Hello! I have 11 .faa files in a folder. I ran orthofinder -d -f /public/home/newfasta -t 64 -o output_orthofinder. But after 13-14 minutes process failed. There is no error. I opened slurm.out file then checked. there was written like below.
Updated 2 months ago
"Invalid escape sequence" errors while starting OrthoFinder
Updated 2 months ago
Duplicates of the same gene in Orthogroup sequence files
Updated 2 months ago3
Inferring gene trees with for orthogroups with less than 4 sequences
Closed 2 months ago1
Issue with rerunning orthofinder "from trees" step -- Blast0_0.txt not found
Updated 2 months ago1
-T raxml-ng——ERROR: Species tree inference failed
Updated 2 months ago
is it possible to specify a tree for orthofinder?
Updated 2 months ago1
Which directories for versions of Orthofinder v2.4.0 (or more recent) are valid with the HOGs?
Updated 2 months ago
ERROR: external program called by OrthoFinder returned an error code: -9
Updated 3 months ago
ValueError: setting an array element with a sequence.
Updated 3 months ago
Identifying number of characters involved in species tree inference using -M msa option
Updated 3 months ago
Get order of concatenated sequences in SpeciesTreeAlignment.fa
Updated 3 months ago
Rooted species tree branch length meaning
Updated 3 months ago1
Orthogroups vs Superfamily Family Tree
Updated 3 months ago
OSError: [Errno 24] Too many open files [32514] Failed to execute script 'orthofinder' due to unhandled exception!
Updated 4 months ago
conda install failes
Updated 4 months ago1
DockerFile
Updated 4 months ago
Only two species comparison, but the number of one-to-one orthologs in Orthologues Stats one_to_one.tsv is more than the number of single-copy orthogroups in statistics Overall.tsv file
Updated 4 months ago
Is it possible to detect Orthologous Isoforms
Updated 4 months ago
ERROR when starting from BLAST, Orthogroups or Tree
Updated 5 months ago
[Feature request] reduce number generated files per directory (e.g. for blast results, pickle files)
Updated 5 months ago
[Bug:] Option `-p tmp_pickle_dir` not working
Updated 5 months ago
Issue with user supplied species tree
Updated 5 months ago
Installing on Mac M1 - README update
Updated 5 months ago
paralogs in same species
Updated 5 months ago
different sets of genes as input
Updated 5 months ago
diamond dropped --ignore-warnings flag, leads to error
Closed 6 months ago5
To run STAG/STRIDE without requiring all species present in tree/ output with only species present in all trees
Closed 6 months ago1
生信分析求助，报错137，ERROR: external program called by OrthoFinder returned an error code: 137
Updated 6 months ago4
ERROR: .fas appears to contain nucleotide sequences instead of amino acid sequences. Use '-d' option
Closed 7 months ago
-M msa -T raxml fails in OrthoFinder 2.5.5
Updated 7 months ago
Orthofinder not writing gene to HOG even though it matches all others in the group
Updated 7 months ago
Running with GLIBC 2.17
Closed 8 months ago
An error is reported when running orthofinder for more than 15 species
Updated 8 months ago
Pan Plot as Roary
Updated 8 months ago
From Orthogroups to a core Proteome
Updated 8 months ago
Broken link to tutorials in README
Updated 9 months ago
Orthogroups.txt and Orthogroups.csv files do not match
Updated 9 months ago1
Orthologic Subfamily identification
Updated 9 months ago
adding and removing proteomes - all-vs-all blast
Updated 9 months ago