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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???

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    $\begingroup$ Thanks, your research objectives are complicated and difficult to answer in a question and answer format, even for a phylogeneticist with experience in bacteria. The other issue is language, because potential typing errors can change the meaning of what you are doing. Lets keep trying, I'm sure we'll get there. $\endgroup$
    – M__ ♦
    Mar 13, 2020 at 6:35
  • $\begingroup$ Okay I'm not really sure so I've bountied your question. Please supply as much information as possible about your 22 contigs, lets see if someone else could anwer this. $\endgroup$
    – M__ ♦
    Mar 14, 2020 at 20:21

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The one thing that strikes me is that OrthoMCL was written under David Roos supervision, which really means it was written with Toxoplasma gondii in mind, i.e. a eukaryotic parasite with notable levels of gene duplication. They tested it against Plasmodium falciparum, but that isn't surprising because both are members of the Apicomplexa. Personally I would suggest looking at a tool more orientated towards bacteria, albeit I'd like to see the output of OrthoMCL.

Prokka is a tool that might give better results, here, which is designed for bacteria, but personally I would extract the orthologes/homologues directly if the primary purpose is to contruct a phylogeny, i.e. I would parse annotated genes which are not "hypothetical".

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    $\begingroup$ Just wanting to add that I've had good experiences with using Orthofinder on bacteria, and it's more user-friendly than I'd have thought possible for something that uses a command line (I'm leaving this as a comment because I've never used OrthoMCL). $\endgroup$
    – Laura
    Mar 17, 2020 at 16:52
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I would say, 120 markers is enough for phylogenetic analysis. see https://gtdb.ecogenomic.org/

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