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hoelzer-lab / ribap

A comprehensive bacterial core gene-set annotation pipeline based on Roary and pairwise ILPs
GNU General Public License v3.0
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Calculate core gene tree #56

Closed hoelzer closed 1 month ago

hoelzer commented 10 months ago

At the moment, we calculate a --tree from all RIBAP groups that have all input species. E.g., when there are 28 input genomes we search for MSAs that have 28 genes in the filter_alignment step.

This can fail when there are no such MSAs, see #54

A solution can be, that we search for MSAs with n-1 species if there are no with n species. However, we need to check how this impacts the core gene MSA and final tree calculations. It can then also happen, that species that were given as input do not show up in the tree (e.g. when there is a species that does not have any core gene with all the other species, but then does a core gene tree anyway make sense?)

hoelzer commented 1 month ago

Should be fixed with a solution in https://github.com/hoelzer-lab/ribap/releases/tag/1.0.2