OrthoFinder v1.1.8
Added Functionality:
- New SingleCopyOrthogroups.txt results file i.e. orthogroups containing only one-to-one orthologues relevant for cross-species comparisons.
- Allow any multiple sequence alignment and tree inference program to be used for inference of gene trees
- New MSA and tree inference tools can be user-added by adding a tool to the config.json file.
- Allow Diamond as a significantly faster alternative to BLAST search. Available on github.
- New Orthogroups.GeneCount.csv results file giving the number of genes per species in each orthogroup, allowing easy plotting of orthogroup results.
- Updated the manual.
As of version 1, automated inference of:
- Orthologues (in addition to previously inferred orthogroups). See Orthogroups, Orthologues & Paralogues.
- Gene trees for all orthogroups
- Rooted species tree
There are extra dependencies need to perform the new (version 1) analyses, please see README file: https://github.com/davidemms/OrthoFinder