Page Index - mlin/PhyloCSF GitHub Wiki

25 page(s) in this GitHub Wiki:

• Home
• PhyloCSF
• Introduction
• Briefly: What the PhyloCSF software does
• PhyloCSF browser tracks
• Obtaining the PhyloCSF software
• 1. Install the OCaml package manager OPAM
• 2. Install dependencies using OPAM
• 3. Download and compile PhyloCSF
• 4. (optional) Run tests
• Preparing alignments
• Available phylogenies
• Running PhyloCSF
• Evaluate a complete ORF (boundaries, strand and reading frame known)
• Evaluate an individual exon (boundaries known, strand and/or reading frame unknown)
• Search for the best ORF within a transcript alignment (boundaries, strand and/or reading frame unknown)
• Command-line options
• Interpreting your results
• Using PhyloCSF-Ψ to increase accuracy, set thresholds, and calculate a p-value
• Batch processing of many alignments
• Parallelization
• Omega Test
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• WishList
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