Skip to content

Latest commit

 

History

History
63 lines (54 loc) · 2.71 KB

README.md

File metadata and controls

63 lines (54 loc) · 2.71 KB
Raw

Example dataset to run edgeHOG

This folder contains an example dataset to test edgeHOG. It has been assembled by extracting for 11 Similiformes genomes from the OMA Jul2023 genomes the genes located on chromosome 12. We therefor do not expect that all genes among all genomes have homologs in this dataset. You would usually use the genes on all chromosomes.

The dataset consists of the following species:

           /-CALJA
          |
          |                               /-MACFA
          |                         /Macaca
          |                        |      \-MACMU
-Simiiformes         /Cercopithecinae
          |         |              |--PAPAN
          |         |              |
          |         |               \-CHLSB
          |         |
           \Catarrhini                  /-PONAB
                    |                  |
                    |          /Hominidae        /-GORGO
                    |         |        |        |
                    |         |        |        |    /-PANPA
                    |         |         \Homininae-Pan
                     \Hominoidea                |    \-PANTR
                              |                 |
                              |                  \-HUMAN
                              |
                               \-NOMLE

The chromosome 12 of these genomes contains the following number of genes:

Genome Scientific name Source Nr Genes
CALJA Callithrix jacchus Ensembl 106 1110
MACFA Macaca fascicularis Ensembl 94 722
MACMU Macaca mulatta Ensembl 106 726
PAPAN Papio anubis Ensembl 106 1275
CHLSB Chlorocebus sabaeus Ensembl 77 706
PONAB Pongo abelii Ensembl 106 1063
GORGO Gorilla gorilla gorilla Ensembl 106 1121
PANPA Pan paniscus Ensembl Main 91 1124
PANTR Pan troglodytes Ensembl Main 91 1149
HUMAN Homo sapiens Ensembl 102 1033
NOMLE Nomascus leucogenys Ensembl 106 1114

We inferred HOGs using FastOMA 0.3.3 using the protein sequences available in sequences.tgz and the species_tree.nwk. The inferred HOGs are available in FastOMA_HOGs.orthoxml.

EdgeHOG can be run using the FastOMA_HOGs.orthoxml file together with the gff3 files (available in gff3/*gff). Again, these contain only the genes located on chromosome 12.

The following command will compute the ancestral edges with edgeHOG:

edgehog  --hog test_data/FastOMA_HOGs.orthoxml \
         --species_tree test_data/species_tree.nwk \
         --gff_directory test_data/gff3/ \
         --date_edges \
         --output_directory test-results