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BenoitMorel / GeneRax

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Availability of Aleml-like (.rec file) output in newick format? #41

Open Jigyasa3 opened 3 years ago

Jigyasa3 commented 3 years ago

Hey all!

I am interested in examining some of the main transfer events in my species tree-gene tree reconciliation, but both .xml and .nhx gives me all the transfer events. I was wondering if it's possible to extract out the reconciliation in Newick format similar to aleml's .rec file that contains the DTL events on the gene tree and species tree?

BenoitMorel commented 3 years ago

Hey Jigyasa3,

I don't understand the difference between "main transfer events" and "all transfer events". Are you interested in the list of newick files in the .rec file or in the other "statistics" provided in the .rec file?

Please keep in mind that ALE outputs several sample gene trees per family, while generax outputs only one (the maximum likelihood tree). I don't know if that's an issue for you.