oggmap/orthomap - example data

Example data for python package oggmap/orthomap.

OrthoFinder:  Ensembl release-105 (-S diamond_ultra_sens)

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:

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

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>

OrthoFinder:  Ensembl release-110 (-S last)

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:

• <ensembl_110_orthofinder_last_Orthogroups.GeneCount.tsv.zip>
• <ensembl_110_orthofinder_last_Orthogroups.tsv.zip>

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

• <ensembl_110_orthofinder_last_species_list.tsv>

Includes NCBI taxonomic tree for Ensembl release-110 species analysed:

• <ensembl_110_species_tree_ncbi_topology_named.nw>
• <ensembl_110_species_tree_ncbi_topology_named.pdf>

OrthoFinder:  Ensembl release-111 (-S last)

Includes OrthoFinder results (-S last) for all translated coding sequences (CDS) from Ensembl release-111 (keeping only longest isoforms) and Xtropicalisv9.0.Named.primaryTrs.pep.fa from www.xenbase.org:

• <ensembl_111_orthofinder_last_Orthogroups.GeneCount.tsv.zip>
• <ensembl_111_orthofinder_last_Orthogroups.tsv.zip>

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

• <ensembl_111_orthofinder_last_species_list.tsv>

OrthoFinder:  Ensembl release-112 (-S last)

Includes OrthoFinder results (-S last) for all translated coding sequences (CDS) from Ensembl release-112 (keeping only longest isoforms) and Xtropicalisv9.0.Named.primaryTrs.pep.fa from www.xenbase.org:

• <ensembl_112_orthofinder_last_Orthogroups.GeneCount.tsv.zip>
• <ensembl_112_orthofinder_last_Orthogroups.tsv.zip>

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

• <ensembl_112_orthofinder_last_species_list.tsv>

OrthoFinder:  WormBase release-WS288 + WormBase ParaSite release-WBPS18 (-S last)

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:

• <WS288_WBPS18_orthofinder_last_Orthogroups.GeneCount.tsv.zip>
• <WS288_WBPS18_orthofinder_last_Orthogroups.tsv.zip>

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

• <WS288_WBPS18_orthofinder_last_species_list.tsv>

Includes NCBI taxonomic tree for WormBase release-WS288 and WormBase ParaSite release-WBPS18 species analysed:

• <WS288_WBPS18_species_tree_ncbi_topology_named.nw>
• <WS288_WBPS18_species_tree_ncbi_topology_named.pdf>

OrthoFinder:  WormBase release-WS293 + WormBase ParaSite release-WBPS19 (-S last)

Includes OrthoFinder results (-S last) for all translated coding sequences (CDS) from WormBase release-WS293,  WormBase ParaSite release-WBPS19 (keeping only longest isoforms):

• <WS293_WBPS19_orthofinder_last_Orthogroups.GeneCount.tsv.zip>
• <WS293_WBPS19_orthofinder_last_Orthogroups.tsv.zip>

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

• <WS293_WBPS19_orthofinder_last_species_list.tsv>

Includes NCBI taxonomic tree for WormBase release-WS293 and WormBase ParaSite release-WBPS19 species analysed:

• <WS293_WBPS19_species_tree_ncbi_topology_named.nw>
• <WS293_WBPS19_species_tree_ncbi_topology_named.pdf>

Pre-calculated orthomaps:

Includes pre-calculated gene age assignments for C. elegans (Sun et al. 2021), H. vulgaris (Cazet et al. 2022) and D. rerio (Ensembl-105; Ensembl-110):

• <Sun2021_Orthomap.tsv>
• <Cazet2022_Orthomap.tsv>
• <zebrafish_ensembl_105_orthomap.tsv>
• <zebrafish_ensembl_110_orthomap.tsv>

Pre-calculated evolutionary indices:

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

• <Ma2021_Fst.tsv>

eggNOG database version 6.0 orthomaps:

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

• <eggnog6_eukaryota_orthomaps.tsv.zip>

myTAI example data:

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

• <PhyloExpressionSetExample.h5ad>

PLAZA database version 5.0 orthomaps:

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>

Mouse synonyms:

Table of Mus musculus gene synonyms obtained from here https://github.com/mustafapir/geneName/blob/master/data/mouse_synonyms1.rda and converted into a table.

• <mouse_synonyms.tsv>