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I have tried to run OrthoFiller.py (v1.1.4) with OrthoFinder version 2.2.7 and 2.3.3 with the sample data. In both cases after OthoFinder finishes I get the following:
`output_folder/sequences/aa
Ca…
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Hello,
I am working with long non-coding rnas of 9 different species and would like to determine how conserved they are. To do this, I did a reciprocal blastn of all possible species combinations …
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- [x] Install and check orthofinder
- [x] Run orthofinder for *C. intermedia* fasta files (RNAseq_SEQs vs model_SEQs)
- [x] Check presence of the 131 unassigned genes (model-related FASTA) in the…
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Can the next release feature a `-o` option to specify the output directory? I ran a batch job of a bunch of runs and had to search a bit to find the working directory. This is also helpful when the d…
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Hello,
I'm testing OrthoFinder with a bunch of assembled genomes/transcriptomes peptides sequences, and the species tree ended to lack support values.
I used the "normal" command-line to run OrthoF…
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Hi, Thank you for building this tool. It is really great and quite user friendly.
What are the advantages or disadvantages of using nucleotide sequences as the input to orthofinder versus using ami…
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The program seems not able to find a file that it should be internally generated:
`grep: path/to/file.fa.proposedGenes: No such file or directory`
(I substituted the original file with path/to/fil…
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In the REFERENCE_pangenes.txt output file, we have 27000 unique orthogroups ('og' column, syntenic and non-syntenic orthologs).
However after running query_pangenes(gsParam, refGenome = "REFERENCE"…
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Hello,
I was wondering if this is possible to use shoot with existing database of multiple alignment and trees.
Let's say that I reproduce the same directories as orthofinder and include diamond d…
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Hi!
I'm using OrthoFinder to infer the evolutionary relationship between different sea slugs (9 species). I run `orthofinder v2.5.4` as shown below. The Species tree obtained (`Species_Tree/Specie…