adapted phylogenomics code to changes in Compara TSV files #16
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JAlvarezJarreta
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Looks good to me so far. Just a couple of minor edits, including reverting a few "unexpected" changes.
Co-authored-by: Jorge Alvarez-Jarreta <jalvarez@ebi.ac.uk>
Co-authored-by: Jorge Alvarez-Jarreta <jalvarez@ebi.ac.uk>
Co-authored-by: Jorge Alvarez-Jarreta <jalvarez@ebi.ac.uk>
Co-authored-by: Jorge Alvarez-Jarreta <jalvarez@ebi.ac.uk>
Co-authored-by: Jorge Alvarez-Jarreta <jalvarez@ebi.ac.uk>
Co-authored-by: Jorge Alvarez-Jarreta <jalvarez@ebi.ac.uk>
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JAlvarezJarreta
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Aug 28, 2025
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The code edits in this PR adapt the scripts in phylogenomics/ to the Compara TSV files downloaded at runtime. The most important change is that now the bulky Plants Multi-species file is used, as only this file contains orthologues for all pairs of plant species. This file is available for the latest release at:
The scripts have been tested on two different clades. For the record, they are mentioned in a book chapter published in 2022: https://link.springer.com/protocol/10.1007/978-1-0716-2067-0_2