PhyloCSF (DNAnexus Platform App)

Phylogenetic analysis of multi-species genome sequence alignments to identify conserved protein-coding regions

This is the source code for an app that runs on the DNAnexus Platform. For more information about how to run or modify it, see http://wiki.dnanexus.com/.

Inputs

• alignments the CrossSpeciesAlignments to evaluate, usually generated by the MAF Stitcher app
• output_name name of the output table
• alignments_per_job controls the degree of parallelization
• species_set usually auto-detected for alignments produced by the MAF Stitcher app
• frames search over three or six reading frames
• orf search over ORFs within each alignment
• min_codons minimum length considered in ORF search mode (with orf != AsIs)

Advanced Inputs

• strategy model and parameter optimization strategy
• all_scores report all scores computed (with frames != 1 or orf != AsIs)
• bls include a Branch Length Score along with PhyloCSF score in output table
• anc_comp include an ancestral composition score along with PhyloCSF score in output table
• dna include evaluated DNA sequence in output table
• aa include evaluated amino acid sequence in output table
• instance_type instance type for parallel jobs

Outputs

• scores
• errors number of alignments without scores (see job log for details)