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:  Ensembl release-113 (-S last)

Includes OrthoFinder results (-S last) for all translated coding sequences (CDS) from Ensembl release-113 (keeping only longest isoforms) and Xtropicalisv9.0.Named.primaryTrs.pep.fa from www.xenbase.org:

• <ensembl_113_orthofinder_last_Orthogroups.GeneCount.tsv.zip>
• <ensembl_113_orthofinder_last_Orthogroups.tsv.zip>

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

• <ensembl_113_orthofinder_last_species_list.tsv>

OrthoFinder:  Ensembl release-114 (-S last)

Includes OrthoFinder results (-S last) for all translated coding sequences (CDS) from Ensembl release-114 (keeping only longest isoforms) and Xtropicalisv9.0.Named.primaryTrs.pep.fa from www.xenbase.org:

• <ensembl_114_orthofinder_last_Orthogroups.GeneCount.tsv.zip>
• <ensembl_114_orthofinder_last_Orthogroups.tsv.zip>

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

• <ensembl_114_orthofinder_last_species_list.tsv>

OrthoFinder:  Ensembl release-115 (-S last)

Includes OrthoFinder results (-S last) for all translated coding sequences (CDS) from Ensembl release-115 (keeping only longest isoforms) and Xtropicalisv9.0.Named.primaryTrs.pep.fa from www.xenbase.org:

• <ensembl_115_orthofinder_last_Orthogroups.GeneCount.tsv.zip>
• <ensembl_115_orthofinder_last_Orthogroups.tsv.zip>

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

• <ensembl_115_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>

Broccoli:  Example (default settings)

Includes Broccoli results (default settings) for translated coding sequences (CDS) from four plant sepcies (keeping only longest isoforms) namely A. lyrata, A. thaliana, C. hirsuta and C. rubella:

• <broccoli_example_table_OGs_protein_counts.txt>
• <broccoli_example_table_OGs_protein_names.txt>

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

• <broccoli_example_species_list.tsv>

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; Ensembl-113):

• <Sun2021_Orthomap.tsv>
• <Cazet2022_Orthomap.tsv>
• <zebrafish_ensembl_105_orthomap.tsv>
• <zebrafish_ensembl_110_orthomap.tsv>
• <zebrafish_ensembl_113_orthomap.tsv>

Pre-calculated Ensembl release-113 orthomaps (OrthoFinder -S last):

Includes extracted orthomaps for all species from Ensembl release-113 based on OrthoFinder (-S last):

• <ensembl_113_orthofinder_last_orthomaps.tsv.zip>

Pre-calculated Ensembl release-114 orthomaps (OrthoFinder -S last):

Includes extracted orthomaps for all species from Ensembl release-114 based on OrthoFinder (-S last):

• <ensembl_114_orthofinder_last_orthomaps.tsv.zip>

Pre-calculated Ensembl release-115 orthomaps (OrthoFinder -S last):

Includes extracted orthomaps for all species from Ensembl release-115 based on OrthoFinder (-S last):

• <ensembl_115_orthofinder_last_orthomaps.tsv.zip>

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>