Requirement of phylogenetic relative

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Tianhua Liao

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Aug 2, 2021, 9:38:54 PM8/2/21
to GeneRax
Dear all,

I have a question on the requirement of the phylogenetic relatives in the species tree.

For example, if I have a gene tree with 500 tips and they came from 400 genomes, should I add more phylogenetic relatives of these 400 genomes on the species tree?  If yes, how much of them is appropriate?

Furthermore, if more genomes that don't contain corresponding genes (present at the given gene trees) were added in the species tree would increase the run time? 

Best regards,
Tianhua

Benoit Morel

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Aug 3, 2021, 3:38:52 AM8/3/21
to Tianhua Liao, GeneRax
Dear Tianhua,

It depends why the gene family has no gene mapped to the genomes you want to add:
- if you think that the new genomes have this gene but that this gene was not sampled (missing data), then adding those genomes might mislead GeneRax
- if you think that the new genome do not have a copy of this gene because the gene was lost during the gene evolutionary history (gene loss), then this can be useful information for GeneRax (although I am not 100% it will help that much)

If you are not sure, I recommend not adding relative genomes that have no gene mapped to them.

To answer your second question, adding more genomes will increase the runtime: for each gene family, the time spent in evaluating the reconciliation likelihood score is proportional to the number of genomes times the number of genes.

Best,
Benoit

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