cahuparo/phylogenomic

Phylogenomic

A) OrthoFinder tools :

i) OrthoFinder-NumberOfGenesPerOrthogroupsPerSpecies.pl

This first R script is working on OrthoFinder ortohogroup matrix "Orthogroups.csv" :

Usage :

./OrthoFinder-CountOrthogroupsPerSpecies.R 
Usage: ./OrthoFinder-CountOrthogroupsPerSpecies.R [options]


Options:
        -f CHARACTER, --file=CHARACTER
                dataset file name

        -o CHARACTER, --out=CHARACTER
                output prefix file name

        -h, --help
                Show this help message and exit

Description : This script is producing a report of the number of genes per orthogroup and per species Dependency : is a matrix with Orthogroup as row (i) and species as column (j) Mij is a list of genes separated by a comma (,)

ii) OrthoFinder--SCOmatrixBuilder.R

This script is filtering orthogroups observed one and only one times per species (Single Copy Orthologs). It needs an ocurrence matrix (as printed by OrthoFinder-NumberOfGenesPerOrthogroupsPerSpecies.pl), as well as three R library ('ggplot2', 'reshape2' and 'optparse')

./OrthoFinder-SCOmatrixBuilder.R 
Usage: ./OrthoFinder-SCOmatrixBuilder.R [options]


Options:
        -f CHARACTER, --file=CHARACTER
                dataset file name

        -o CHARACTER, --out=CHARACTER
                output prefix file name

        -h, --help
                Show this help message and exit

Two types of files is produced : a list of orthogroups ids in "*.list" and a graphical representation of genes presence/absence by species. This two files is produced for SCO observed at least in 75% of species, 50% and 37.5%.

iii) Super alignment builder (concatenation with partition)

This R script is concatenating multiple alignements, creating a partition file (ready to use by RAxML), reporting empty alignements and producing a visual report of the super-alignment.

Usage: ./ConcatAlignement.R [options]


Options:
        -f CHARACTER, --file=CHARACTER
                SCOlist file name

        -o CHARACTER, --out=CHARACTER
                output alignement prefix

        -h, --help
                Show this help message and exit