I obtained a SNP list (VCF format) from a sample's transcriptome (assembled by Trinity). ORFs were identified using TransDecoder. How I classify these SNPs? How to calculate ka/ks？
You can annotate VCFs using SnpEFf, but you will first have to build the database: http://snpeff.sourceforge.net/SnpEff_manual.html#databases
This will (in the end) make a new VCF with non-synonymous SNPs and their severity (introduces STOP codons, changes AA, changes nothing etc.). SNPEff's report will also report the total number of Ka and Ks, if I remember correctly.
If you want to calculate Ka/Ks on a more detailed scale, use this script: https://github.com/MerrimanLab/selectionTools/blob/master/extrascripts/kaks.py which takes SNPEff's output and gives out a Ka/Ks table per gene
