Gene Gain/loss + Duplication Tree

Question

[moranr]

Hi,

Is there a tool to carry out gene gain loss + duplication analysis with the HOGs, like this: http://imgur.com/XuIGhnj (from the paper).

If not, can you give an indication to how you created this image?

Thanks,
R

Answer 1

[Adrian Altenhoff]

Hi moranr,

the analysis to collect the data for these figures has been done using family-analyzer https://github.com/DessimozLab/familyanalyzer. It's a tool to mind orthoxml files in general in terms of the gene gains- and lost events. As input it requires an orthoxml file defining HOGs, e.g. the output from OmaStandalone http://omabrowser.org/standalone.

Best
Adrian

[moranr]

Fantastic, Thank you.