orthomap - example data

Example data for python package orthomap. <strong>OrthoFinder: Ensembl release-105 (-S diamond_ultra_sens)</strong> Includes OrthoFinder results (-S diamond_ultra_sens) for all translated coding sequences (CDS) from Ensembl release-105 (keeping only longest isoforms) and Xtropicalisv9.0.Named.primaryTrs.pep.fa from www.xenbase.org: &lt;ensembl_105_orthofinder_Orthogroups.GeneCount.tsv.zip&gt; &lt;ensembl_105_orthofinder_Orthogroups.tsv.zip&gt; Includes a table specifying the OrthoFinder species file names and its corresponding NCBI taxonomic IDs: &lt;ensembl_105_orthofinder_species_list.tsv&gt; Includes NCBI taxonomic tree for Ensembl release-105 species analysed: &lt;ensembl_105_species_tree_ncbi_topology_named.nw&gt; &lt;ensembl_105_species_tree_ncbi_topology_named.pdf&gt; <strong>OrthoFinder: Ensembl release-110 (-S last)</strong> Includes OrthoFinder results (-S last) for all translated coding sequences (CDS) from Ensembl release-110 (keeping only longest isoforms) and Xtropicalisv9.0.Named.primaryTrs.pep.fa from www.xenbase.org: &lt;ensembl_110_orthofinder_last_Orthogroups.GeneCount.tsv.zip&gt; &lt;ensembl_110_orthofinder_last_Orthogroups.tsv.zip&gt; Includes a table specifying the OrthoFinder species file names and its corresponding NCBI taxonomic IDs: &lt;ensembl_110_orthofinder_last_species_list.tsv&gt; Includes NCBI taxonomic tree for Ensembl release-105 species analysed: &lt;ensembl_110_species_tree_ncbi_topology_named.nw&gt; &lt;ensembl_110_species_tree_ncbi_topology_named.pdf&gt; <strong>OrthoFinder: WormBase release-WS288 + WormBase ParaSite release-WBPS18 (-S last)</strong> Includes OrthoFinder results (-S last) for all translated coding sequences (CDS) from WormBase release-WS288, WormBase ParaSite release-WBPS18 (keeping only longest isoforms) and dd_Smed_v6.pcf.contigs.fasta (transdecoder and miniprothint peptides) from https://planmine.mpibpc.mpg.de: &lt;WS288_WBPS18_orthofinder_last_Orthogroups.GeneCount.tsv.zip&gt; &lt;WS288_WBPS18_orthofinder_last_Orthogroups.tsv.zip&gt; Includes a table specifying the OrthoFinder species file names and its corresponding NCBI taxonomic IDs: &lt;WS288_WBPS18_orthofinder_last_species_list.tsv&gt; Includes NCBI taxonomic tree for WormBase release-WS288 and WormBase ParaSite release-WBPS18 species analysed: &lt;WS288_WBPS18_species_tree_ncbi_topology_named.nw&gt; &lt;WS288_WBPS18_species_tree_ncbi_topology_named.pdf&gt; <strong>Pre-calculated orthomaps:</strong> Includes pre-calculated gene age assignments for <em>C. elegans</em> (Sun et al. 2021), <em>H. vulgaris</em> (Cazet et al. 2022) and <em>D. rerio</em> (Ensembl-105): &lt;Sun2021_Orthomap.tsv&gt; &lt;Cazet2022_Orthomap.tsv&gt; &lt;zebrafish_ensembl_105_orthomap.tsv&gt; <strong>Pre-calculated evolutionary indices:</strong> Includes pre-calculated TajimaD, NormalizedPi, FayWu, Fst for C. elegans (Ma et al. 2021): &lt;Ma2021_Fst.tsv&gt; <strong>eggNOG database version 6.0 orthomaps:</strong> Includes extracted orthomaps for all Eukaryota from eggNOG database version 6.0 (Hernández-Plaza et al. 2022): &lt;eggnog6_eukaryota_orthomaps.tsv.zip&gt; <strong>myTAI example data:</strong> Includes example data from the myTAI R package (Drost et al. 2018) &lt;PhyloExpressionSetExample.h5ad&gt; <strong>PLAZA database version 5.0 orthomaps:</strong> Includes extracted orthomaps for either HOMFAM or ORTHOFAM groups of plants from PLAZA database version 5.0 (Van Bel et al. 2022): &lt;plaza_v5_dicots_HOMFAM_orthomaps.tsv.zip&gt; &lt;plaza_v5_dicots_ORTHOFAM_orthomaps.tsv.zip&gt; &lt;plaza_v5_monocots_ORTHOFAM_orthomaps.tsv.zip&gt; &lt;plaza_v5_monocots_ORTHOFAM_orthomaps.tsv.zip&gt; <strong>Mouse synonyms:</strong> Table of <em>Mus musculus</em> gene synonyms obtained from here https://github.com/mustafapir/geneName/blob/master/data/mouse_synonyms1.rda and converted into a table. &lt;mouse_synonyms.tsv&gt;