Non-synonymous (Ka) and synonymous (Ks)

Non-synonymous (Ka) and synonymous (Ks) substitution rates are estimated using the Nei-Gojobori method implemented in the YN00 program in the PAML (4.9h)

Parameters

Parameters	Standards and instructions
cds_file	Type: file | Default: - A cds file of one or more genomes.
pep_file	Type: file | Default: - A protein file for one or more genomes.
align_software	Type:{ muscle, mafft } | Default: muscle Software of multiple sequence alignment.
pairs_file	Type: file | Default: - Colinearscan or MCScanX result file or gene pairs divided by tab.
ks_file	Type: file | Default: - The output file name of ks.

Use command to enter the folder wgdi -ks ? >> total.conf Take out the parameter file.

[ks]
cds_file = cds file
pep_file = pep file
align software = muscle
pairs_file = gene  pairs file
ks_file = ks result

Quick start

After the parameters are modified properly, then run wgdi -ks total.conf

Example

The original results are easily accessible at wgdi-example