Visualizing the final amalgamated reconciliation in recphyloXML

Alejandro Gil Gomez

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May 9, 2024, 1:15:24 PM5/9/24

to GeneRax

Hello Benoit,

I was wondering if it is possible to get a recphyloXML for the final amalgamated reconciliation to visualize the output in thirdkind. I really like the rec_uml output with all the node information, but it would also be helpful to see the result of the best reconciliation for multiple orthogroups combined into a single figure.

Thanks again for all your help developing this project.

Best, Alex.

Benoit Morel

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May 10, 2024, 2:39:57 AM5/10/24

to Alejandro Gil Gomez, GeneRax

Hi Alex,

I think that it's kind of possible with Thirdkind but that the output looks very messy with many samples. Implementing reconciliation viewers is very tricky and there is still a lot of progress to be made there...

I have left academia, so I won't have the occasion to work on this. But you can try to contact Simon Penel, who developed Thirdkind, to see if he has any advice for you.

Best,

Benoit

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