I ran the orthomcl program with genomes of the whole streptomyces genus(from ncbi) as input, but I only got 22 orthologous groups(streptomyces's genome size vary from 2M to 15M, which shows the great difference among them). And the analyst from the bioinformatics company told me that my result wasn't reasonable if I try to construct the phylogenetic tree with the 22 orthologous groups I got. He also told me, I'd better use almost 1000 orthologous groups to build the tree. My question is, how to know my orthologous groups are enough to construct a tree?
The program was run during my summer vacation(a long time ago...), but I still can't realize why "1000 orthologous groups are needed". And the analyst form company just tell me that it was the experience number. But when I read some article about comparative genomics, I see some papers are used just about 10 single-copy genes to build the tree, why???