Florent Lassalle

incomplete event reporting with NHX reconciliated tree format

2

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...

When `$updatefromdb` variable is set i.e. when calling `pantagruel` with the `-u|--update_from` option, at the moment, only protein families defined during task `01` are made to match the protein/gene family...

Branch `usingGeneRax` is still unstable (unfinished) at the final stages: need to complete the scripts for processing GeneRax output for integration of reconciliation results into the Pantagruel database (for querying...

It would be great to be able to provide as input a query string as used in the NCBI Entrez system to automatically generate the list of assemblies to download,...

unable to make Sirius use Gurobi solver

2

Hi, I have been trying (quite hard) to make Sirus use Gurobi as the iLP solver instead of the built-in CLP, but so far to no avail. Could you please...