GeneRax
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BenoitMorel
This should not affect the documented features of GeneRax, but we should nonetheless fix it!
In particular, it is very difficult for users to count the number of extinctions per species, because the losses are only detected as SL events at the parent level. See...
See discussion here https://groups.google.com/g/generaxusers/c/p5vph7ytOnU/m/tlnZSPCnCwAJ
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....
Hi Benoit, I am implementing a parse for GeneRax output, and specifically the reconciled tree in NHX format as that's how they come out of the program with the `--reconciliation-samples`...
Hi Benoit, I first wanted to confirm that v1.2.0 works well, with scenarios that make sense and no bugs. Well done! Only one thing I found was not correct was...
Hello, I receive a `Cannot read alignment file (file exists but is invalid)` error whenever I try to use a "Q" model following RAXML syntax (Q.pfam, Q.insect, Q.yeast, etc.) is...
Hi there! I am having an issue with achieving the duplication and loss rates for my dataset. I have 7-10 distantly related species (>200 MYA divergence time) for each and...
Hi Benoit, I am trying to build GeneRax on an Ubuntu virtual machine but I am having the following error: "make: *** [Makefile:91: all] Error 2". I have copied the...
Hi! I have been encountering the following issue: I am running generax on my university's high performance computing platform where I have a maximum amount of time I am allowed...