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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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Using Orthofinder to find horizontal gene transfer #316

Closed scubapenn closed 4 years ago

scubapenn commented 4 years ago

Would orthofinder be able to find fin orthologs one of which which was acquired via HGT?

davidemms commented 4 years ago

Yes, in many cases it will be able to as OrthoFinder doesn't rely on the gene tree and species tree agreeing in order to identify orthologs. Additionally, if you have high enough species sampling then OrthoFinder should also be able to identify that the gene is not where it is expected in the gene tree, identify that it is a putative HGT and identify that the related genes are xenologs and put these relationships in the Putative_Xenologs/ directory.

All the best David

mtnouchi commented 4 years ago

Hello,

I have a question for this topic. As far as I understand, OrthoFinder uses DLCpar for reconciliation and DLCpar only models duplication, loss and deep coalescence but not transfer.

How does OrthoFinder infer HGTs when DLCpar does not assume transfer events unlike other reconciliation algorithms such as ranger-dtl?

Regards,

davidemms commented 4 years ago

Hi

DLCpar was only used a few years ago, in an early version of the orthologs from gene trees functionality. It wasn't accurate enough and so was replaced with a new algorithm, described in the latest paper: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1832-y

The current version identifies 'Phylogenetically Misplaced Genes" as an additional step. At the moment I would still call this prototype functionality. Its purpose is to avoid missing true orthologs within the gene trees because of genes that appear to be out of place in the gene tree, given knowledge of the species tree. In a number of cases I've looked at the source of many of these genes is contamination, and thus identifying them is useful. If you are looking for HGTs then these genes are a good place to start but that's not its main goal

All the best David

mtnouchi commented 4 years ago

Thank you for letting me know the new algorithm and giving some advice to find HGTs! I'll keep in mind that it would be prototype functionality. But this information is really helpful for me!