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Published October 23, 2022 | Version 0.0.6
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orthomap - example data

Creators

  • 1. Max Planck Institute for Evolutionary Biology

Contributors

Project leader:

  • 1. Max Planck Institute for Evolutionary Biology

Description

Example data for python package orthomap.

Includes OrthoFinder results 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:

  • <ensembl_105_orthofinder_Orthogroups.GeneCount.tsv.zip>
  • <ensembl_105_orthofinder_Orthogroups.zip.tsv>

Includes a table specifying the OrthoFinder species file names and its corresponding NCBI taxonomic IDs:

  • <ensembl_105_orthofinder_species_list.tsv>

Includes NCBI taxonomic tree for Ensembl release-105 species analysed:

  • <ensembl_105_species_tree_ncbi_topology_named.nw>
  • <ensembl_105_species_tree_ncbi_topology_named.pdf>

Includes pre-calculated gene age assignments for C. elegans (Sun et al. 2021) and H. vulgaris (Cazet et al. 2022):

  • <Sun2021_Orthomap.tsv>
  • <Cazet2022_Orthomap.tsv>

Includes pre-calculated TajimaD, NormalizedPi, FayWu, Fst for C. elegans (Ma et al. 2021):

  • <Ma2021_Fst.tsv>

Includes extracted orthomaps for all Eukaryota from eggNOG database version 6.0 (Hernández-Plaza et al. 2022):

  • <eggnog6_eukaryota_orthomaps.tsv.zip>

Includes example data from the myTAI R package (Drost et al. 2018)

  • <PhyloExpressionSetExample.h5ad>

Includes extracted orthomaps for either HOMFAM or ORTHOFAM groups of plants from PLAZA database version 5.0 (Van Bel et al. 2022):

  • <plaza_v5_dicots_HOMFAM_orthomaps.tsv.zip>
  • <plaza_v5_dicots_ORTHOFAM_orthomaps.tsv.zip>
  • <plaza_v5_monocots_ORTHOFAM_orthomaps.tsv.zip>
  • <plaza_v5_monocots_ORTHOFAM_orthomaps.tsv.zip>

Files

eggnog6_eukaryota_orthomaps.tsv.zip

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Additional details

References

  • Emms, D.M. and Kelly, S., 2019. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome biology, 20(1), pp.1-14.
  • Sun, S., Rödelsperger, 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.
  • Hernández-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.