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<p><span style="font-weight: 400;">Hello,</span></p>

<p><span style="font-weight: 400;">For release 116, we are updating the README for homologies made available via Ensembl FTP in TSV format.</span></p>

<p><span style="font-weight: 400;">For Ensembl Vertebrates:</span></p>

<p><a href="https://ftp.ebi.ac.uk/pub/ensembl/current_tsv/ensembl-compara/homologies/"><span style="font-weight: 400;">https://ftp.ebi.ac.uk/pub/ensembl/current_tsv/ensembl-compara/homologies/</span></a><span style="font-weight: 400;"> </span></p>

<p><span style="font-weight: 400;">For Ensembl Genomes (plants for example):</span></p>

<p><a href="https://ftp.ebi.ac.uk/pub/ensemblgenomes/plants/current/tsv/ensembl-compara/homologies/"><span style="font-weight: 400;">https://ftp.ebi.ac.uk/pub/ensemblgenomes/plants/current/tsv/ensembl-compara/homologies/</span></a></p>

<p><span style="font-weight: 400;">Among other things, the updated README clarifies the differences between the homology TSV files at the top level in the 'homologies' directory (each of which stores all available homologies for a given gene-tree collection) and the genome-specific homology TSV files within subdirectories named for a particular genome (each storing an arbitrary subset of homologies involving the given genome).</span></p>

<p><span style="font-weight: 400;">The way in which homologies are stored in genome-specific TSV files has implications for accessing them. To access all available orthologies between two or more genomes (e.g. 'drosophila_melanogaster' and 'saccharomyces_cerevisiae'), you will need to download the genome-specific files of all relevant genomes (e.g. 'drosophila_melanogaster/Compara.116.protein_default.homologies.tsv.gz' and 'saccharomyces_cerevisiae/Compara.116.protein_default.homologies.tsv.gz').</span></p>

<p><span style="font-weight: 400;">An example script is available to illustrate how homologies in genome-specific TSV files may be accessed:</span></p>

<p><span style="font-weight: 400;"><a href="https://github.com/Ensembl/ensembl-compara/blob/release/116/scripts/examples/get_hom_tsv.py">https://github.com/Ensembl/ensembl-compara/blob/release/116/scripts/examples/get_hom_tsv.py</a></span><span style="font-weight: 400;"></span></p>

<p><span style="font-weight: 400;">This README will be included in Ensembl 116 release dumps, but you can already check out the README.gene_trees.tsv_dumps.txt file on GitHub:</span></p>

<p><span style="font-weight: 400;"><a href="https://raw.githubusercontent.com/Ensembl/ensembl-compara/refs/heads/release/116/docs/ftp/README.gene_trees.tsv_dumps.txt">https://raw.githubusercontent.com/Ensembl/ensembl-compara/refs/heads/release/116/docs/ftp/README.gene_trees.tsv_dumps.txt</a></span><span style="font-weight: 400;"></span></p>

<p><span style="font-weight: 400;">All the best,</span></p>

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<p class="v1MsoNormal"><strong><span>Thomas Walsh</span></strong></p>

<p class="v1MsoNormal"><strong>Senior Bioinformatician, Ensembl Compara</strong></p>

<p class="v1MsoNormal"><span>European Bioinformatics Institute (EMBL-EBI)</span></p>

<p class="v1MsoNormal"><span>Wellcome Genome Campus</span></p>

<p class="v1MsoNormal"><span>Hinxton</span></p>

<p class="v1MsoNormal"><span>Cambridge CB10 1SD</span></p>

<p class="v1MsoNormal"><span>United Kingdom</span></p>

<p class="v1MsoNormal"><span>Email: twalsh@ebi.ac.uk</span></p>

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