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