In this repository you find several scripts that form a small pipeline to process aligned core-genes. Clone the repository if you find it interesting and modify the scripts for your own use.
The pipeline calculate the pairwise dN/dS ratio's between all the genes in an alignment in order to determine if there is positive or purifying selection found between the genes of a species of interest.
The genes need to have a nucleotide similarity between 70 and 95 % to give meaningful results. That will mostly be highly consevered genes.
The program Get_homologues can be use to determine the core-genes of a species using a nucleotide cut-off and outputs for each core-genes a fasta file with unaligned sequences
The unaligned sequences can be aligned using PRANK and the alignments need to by in the PHYLIP format *.phy
The pipeline needs several dependencies:
The evolutionary package: PAML
Biopython
Biopython package: Bio.Phylo.PAML
The PAML package is used for the program yn00, which calculates the dN/dS ratio's and this program is called from the python script: pw_flow.py.. That script produces for every dN/dS method available and line with the results for each pairwise comparison. That line is written to a text-file, that collects all the pair-wise comparisons of all core-genes analyzed. In addition, will ot output a text file with the normal yn00 output
The bash file: Yn00Script_batch.sh is placed in the folder (or your PATH) with all the aligned core-genes files. This script will can be run like any normal bash script.
The file: yn00.ctl is created for each gene by the script pw_flow.py. and is needed to run the yn00 program.
The files in this repository.
Yn00Script_batch.sh
pw_flow.py
yn00.ctl
Thomas H.