orthologr
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drostlab
Genome wide orthology inference and dNdS estimation
When using `blast_rec`, headings in _blastresult_{query}.fasta_ and _blastresult_{subject}.fasta_ are not included. I suppose they are the same as output from blast_rec. Right?
Hi @drostlab, I'm trying to set up `orthologr` for detection of orthologs in multiple species. I've installed `orthofinder` into my PATH using `conda install orthofinder`. Calling `orthofinder -h` from `terminal`...
Hello, I'm running dNdS() on the cds of 2 species containing 13486 orthologous pairs, but only 1754 genes get the calculations done for. The rest runs into this error. `ERROR:...
Trying out the `orthologr` package on a system where I cannot do root, either pw or sudo, etc. Installed blast and others to `~/bin` In the docs, it purports to...
I was trying to get the longest isoform from ensemble genomesbut the function is exiting with an error Error: Gene_ID or Peptide_IDs between the gtf file and the headers of...
Hi @HajkD , I'm using the `orthologs` function with `ortho_detection = "RBH"` to detect orthologs for a `query_file` containing 8 protein fasta sequences in multiple `subject_files`. For easier downstream data...
Hi! I just first wanted to say thank you so much for developing this package. It is quite handy and overall greta resource for so many. I've been using the...
CDS file could not be read properly, Please make sure the file contains only CDS sequences and is in fasta format. I have check the filed is in CDS sequence....
When I am using the divergence_stratigraphy function with ds.value = FALSE, as follows: `result
Hello, I am using the orthologr function `retrieve_longest_isoforms()` on both refseq annotations and submitter/non-refseq annotations available on NCBI. I have lists of species IDs, e.g., Dmel, and their corresponding accessions,...
