PhyloCSFpp
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cpockrandt
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.
Hello, I've installed PhyloCSF++ using conda in a newly created environment. I then launched it using ``` phylocsf++ build-tracks --output-raw-phylo 1 \ --output-regions 1 --genome-length 143726002 --coding-exons ./model/coding_exons.txt \ --threads...
Hi, I'm interested in running PhyloCSF++ with annotate-with-mmseqs on Chinese hamster, but I am getting an error when it reaches the _mmseqs createsubdb_ step: ` ./phylocsf++ annotate-with-mmseqs --threads 35 --output...
- [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...
Hi, I work on plants, which seem to be lacking with the precomputed MSAs available. What software would you recommend for creating genome scale MSAs of plants ? I can...
Hi, dear developer, I want to score a single alignment with `phylocsf++` as shown below. However, the output file only contains headers and scores were not calculated. Is there something...
Hi, I cannot run the program with a fasta alignment file, should I only use maf format? Also, if I use publicly available https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz100way/maf/chr1_KI270707v1_random.maf.gz as ```maf``` and run ```phylocsf++ build-tracks...
Hi there, Thanks for building this great tool! I was wondering if PhyloCSF++ can be used to predict CDS regions for RNA fusions? I have RNA gene fusions for which...
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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.