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davidemms / OrthoFinder

Phylogenetic orthology inference for comparative genomics
https://davidemms.github.io/
GNU General Public License v3.0
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Inferring gene trees with for orthogroups with less than 4 sequences #897

Closed niconps14 closed 6 months ago

niconps14 commented 6 months ago

Is there any way for OrthoFinder to infer gene trees for the orthogroups with less than 4 sequences?

Jonathan-Holmes-Bioinformatics commented 6 months ago

Hi niconps14,

Orthofinder can only generate trees from orthogroups containing 4 or more genes. Due to limits introduced by the tree building software used to construct the gene trees (such as RAXML have a minimum input of 4 genes).

Orthofinder will generate the sequences fills for orthogroups of sequence number < 4, so you can generate the trees yourself, but these gene trees may not be meaningful with such a low number of leaves.

Thanks, Jonathan