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PhyloCSFpp
PhyloCSF++ computes PhyloCSF tracks for whole-genome multiple sequence alignments, scores single MSA, annotates CDS features in GFF/GTF files with PhyloCSF and confidence scores.
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TODO
#1
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cpockrandt
opened
3 years ago
cpockrandt
commented
3 years ago
[x] add clang support
[x] add tests for gtf annotation to travis
[ ] Option
--dry
: tells which species cannot be mapped. suggest which model is the best and outputs a
--species
string to speed up computation
[x] weighted mean PhyloCSF scores instead of the mean score in annotation tools
[ ] maf format: support tab-separation and missing scores (i.e. "a\n" lines)
[ ] print output file path instead of just "Done"
[ ] Check other libraries other than cblas, such as OpenBLAS
@martin-steinegger Can you look into this:
[ ] FAQ in wiki for annotate-with-mmseqs
[ ] add mmseqs params in phylocsf++ and forward them to mmseqs
--dry: tells which species cannot be mapped. suggest which model is the best and outputs a--speciesstring to speed up computation@martin-steinegger Can you look into this: