Full readme at https://github.com/davidemms/OrthoFinder/blob/master/README.md Summary sketch at https://github.com/davidemms/OrthoFinder/blob/master/OrthoFinder-manual.pdf
OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics. It finds orthologues and orthogroups infers gene trees for all orthogroups and infers a rooted species tree for the species being analysed. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. OrthoFinder is simple to use and all you need to run it is a set of protein sequence files (one per species) in FASTA format (Emms, D.M. and Kelly, S., 2015).
This galaxy tool implements the first part of the Orthofinder program, e.g. the clustering of orthogroups of genes.
If you have already ran OrthoFinder, the tool allows to re-run the analysis from the pre-computed blast-results.
- When using "from fasta" option (e.g Orthofinder from scratch) : the input files are a set of proteomes in fasta format (on file per species). Choose this option if you have no OrthoFinder results yet.
- When using "from blast results" option : the input files are all the following files from of a previous OrthoFinder run (these files appear only if you have chosen to keep them while launching a previous run):
- A dataset collection / multiple datasets for the blast outputs
- A dataset collection / multiple datasets for .fa files
- The SpeciesIDs.txt file
- The SequencesIDs.txt file
- Sequence search program : You can choose either blast, blast_gz, diamond, or diamond ultra-sensitive (diamond is faster)
- Get the blast results : Check "Yes" if, while using blast as the sequence search program, you want to retrieve the blast output files
- Inflation : the inflation parameter; modify this parameter is not recommended.