Summary
Name
Gene families identification with Orthofinder workflow
Description

OrthoFinder

Identifies orthologous protein sequence families. OrthoFinder provides a three-steps method that first perform orthogroup inference, then, it deduces rooted species and gene trees for lastly determine orthologs and gene duplication events from these rooted gene trees. The application is able to produce a wide of outputs including orthogroups and their gene trees, the rooted species tree, gene duplication events, as well as comparative genomics statistics. [source : omictools]

workflow orthofinder

More informations : https://github.com/davidemms/OrthoFinder/blob/master/README.md

 

Proteomes used in this analysis :

 

Organism

Annotation version

Source file

Arabidopsis thaliana TAIR10 Athaliana_167_TAIR10.protein.fa
Brachypodium distachyon JGIv3.1 Bdistachyon_314_v3.1.protein.fa
Miscanthus sinensis JGIv7.1 Msinensis_497_v7.1.protein.fa
Oryza sativa ssp. japonica MSU7  
Setaria italica JGIv2.2 Sitalica_312_v2.2.protein.fa
Panicum virgatum JGIv1.1 Pvirgatum_273_v1.1.protein.fa
Sorghum bicolor JGIv3.1 Sbicolor_313_v3.1.protein.fa
Zea mays AGPv4 Zea_mays.B73_RefGen_v4.pep.all.fa

 

Program, Pipeline, Workflow or Method Name
OrthoFinder
Program Version
v2.2.1
Algorithm
DIAMOND or MMseqs2, MCL, FastME
Date Performed
Friday, May 4, 2018
Data Source
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