Skip to content

OrthoFinder v2.2.0
Compare
Choose a tag to compare
@davidemms davidemms released this 19 Feb 16:07
· 396 commits to master since this release
2.2.0
0ea93ae

OrthoFinder version 2
The next paper describing the new functionality will be out soon.

New to version 2:

  • Improved orthologues from gene trees inference method: A new method has been implemented that replaces dlcpar as the default. The new method is both significantly faster and more accurate. This is achieved by focusing analysis only on nodes of the gene tree that affect orthologue inference (large trees now analysed in second rather than hours).
  • The orthologue accuracy has been benchmarked with the community Quest for Orthologs service and the results can be seen on their website.
  • Our newly published method, STRIDE: Species Tree Root Inference from Gene Duplication Events, has been integrated for rooting of the species tree.
  • The species tree inference method has been updated, "STAG: Species Tree Inference from All Genes"
  • A new results table of all gene duplication events for each branch of the species tree is provided. The duplication events are cross-referenced to the gene trees, the support for each is quantified, and the ones meeting the stringent STRIDE checks are marked.
  • Consider using the Diamond option instead of BLAST. The benchmarks show that the accuracy is similar (see link above) but DIAMOND is incredibly fast!

New to this release

  • Performance and RAM improvements for large datasets
  • Identify horizontally transferred genes
  • Improved rooting of gene trees
  • Improved identification of orthologues from gene trees
Assets 4
Loading