DOI: 10.5281/zenodo.8366021
title: orthomap - example data

description: 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;
description: {"references": ["Emms, D.M. and Kelly, S., 2019. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome biology, 20(1), pp.1-14.", "Sun, S., R\u00f6delsperger, C. and Sommer, R.J., 2021. Single worm transcriptomics identifies a developmental core network of oscillating genes with deep conservation across nematodes. Genome research, 31(9), pp.1590-1601.", "Cazet, J., Siebert, S., Little, H.M., Bertemes, P., Primack, A.S., Ladurner, P., Achrainer, M., Fredriksen, M.T., Moreland, R.T., Singh, S. and Zhang, S., 2022. New Hydra genomes reveal conserved principles of hydrozoan transcriptional regulation. bioRxiv.", "Hern\u00e1ndez-Plaza, A., Szklarczyk, D., Botas, J., Cantalapiedra, C.P., Giner-Lamia, J., Mende, D.R., Kirsch, R., Rattei, T., Letunic, I., Jensen, L.J. and Bork, P., 2022. eggNOG 6.0: enabling comparative genomics across 12 535 organisms. Nucleic Acids Research.", "Drost, H.G., Gabel, A., Liu, J., Quint, M. and Grosse, I., 2018. myTAI: evolutionary transcriptomics with R. Bioinformatics, 34(9), pp.1589-1590.", "Van Bel, M., Silvestri, F., Weitz, E.M., Kreft, L., Botzki, A., Coppens, F. and Vandepoele, K., 2022. PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants. Nucleic Acids Research, 50(D1), pp.D1468-D1474.", "Ma, F., Lau, C.Y. and Zheng, C., 2021. Large genetic diversity and strong positive selection in F-box and GPCR genes among the wild isolates of Caenorhabditis elegans. Genome Biology and Evolution, 13(5), p.evab048."]}