Question: Clarification of OMA tree metrics
gravatar for samche42
5 weeks ago by
samche420 wrote:


I've used OMA 2.2.0 standalone to generate an estimated species tree from 34 genomes. The tree was successfully generated but I can't seem to find any explanations for the numbers on the tree. Are the node numbers the bootstrap values? Levels of similarity? And the scale bar? Is that a reflection of site substitutions? Difference between HOGs of some sort? I'm so sorry if this is a fundamental question but my googling has failed me.

Thanks in advance for anyone out there that could help me out! :)

species tree oma orthologs • 96 views
ADD COMMENTlink modified 5 weeks ago by adrian.altenhoff440 • written 5 weeks ago by samche420
gravatar for adrian.altenhoff
5 weeks ago by
adrian.altenhoff440 wrote:


I assume you refer the tree in Output/EstimatedSpeciesTree.nwk (or since OmaStandalone 2.3.0 also in phyloxml format). The numbers are branch lengths in PAM (point accepted mutations).

This tree is a relative crude estimate of the underlying species tree but usually good enough for us to infer Hierarchical Orthologous Groups (HOGs) which need a guide tree. The main problem there is if it is wrongly rooted.

If you would like to estimate a good quality species tree we suggest to use the OMAGroups as marker genes and build a tree from a super matrix of them. We provide in Output/OrthologousGrpupsFasta/ for each marker gene a fasta file with unaligned sequences, so you can build MSAs with your favorite tool, build a supermatrix and estimate a phylogenetic tree with your method of choice.

Regards Adrian

ADD COMMENTlink written 5 weeks ago by adrian.altenhoff440

Thank you!! i really appreciate the help :)

ADD REPLYlink written 5 weeks ago by samche420
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