I'm running analysis with OrthoFinder and it produces a single-copy gene tree. When I visualize the tree with iTOL, there's no bootstrap value on the branches or nodes. There's a published paper in BMC Genomics that also didn't show the bootstrap value using OrthoFinder.


  1. Does anybody know why there's no bootstrap values present on the phylogeny?
  2. How can this be corrected?



1 Answer 1


Please check the file

 `$PWD/SpeciesTree_unrooted.txt" `

You should find the bootstrap support* values per branch there. If not make sure is the latest version is installed from https://github.com/davidemms/OrthoFinder

The papers are: genomebiology.biomedcentral.com/articles/10.1186/… and genomebiology.biomedcentral.com/articles/10.1186/… Genome Biology 16:157 ... It officially offers tree stats: "OrthoFinder also provides comprehensive statistics for comparative genomic analyses"

The documentation is here

The question was raised how to increase replicates by one, two or three logs. This is not really orthodox technique. The way the issue should be first addressed is the user performs replicates manually, e.g. 10 new runs, and then looks across the consistency of bootstrap values for each manual replicate. If all values of interest between manual replicates are >80% or <70% it really doesn't matter. However if a key branch ranges from 70 - 75% that is strictly unresolved and would generally be resolved using an alternative test. If the variation is >= 10% that would need addressing. Generally variation between replicates is very low =< 2%

  • note, the original answer just contained the word 'support' and has now been more correctly described as "bootstrap support". Thanks to the OP for pointing this out in the comments below.
  • $\begingroup$ I see, thanks! If I wanna know the bootstrap number, where could I see it? Can I customize the bootstrap number to something like 10000? $\endgroup$
    – raysteven
    Jan 30, 2022 at 2:44
  • $\begingroup$ The file I mentioned contains bootstrap values. I have modified the post to provide the link to the documentation where it describes this. It is under the header 'species tree'. Increasing the bootstrap replicaties is has been answered in the modified post. $\endgroup$
    – M__
    Jan 30, 2022 at 14:23

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