I have total 14 strains of rickettsia species and completed the whole genome sequencing. After that I performed comparative genome analysis to find out the SNP and in-del and found very low number of SNP and also identify Synonymous and non synonymous substitution.Now I want to identify the synonymous and non synonymous site of the whole genome bacterial sequence. As I have low number of SNP it is very difficult to use the PAML package. Is there any simple way to find out the synonymous and non synonymous site easily?
If you have a variant call file from your WGS analysis, you can easily use SNPeff against your reference genome of interest. See http://snpeff.sourceforge.net/
A simple hack would be extracting 100 nt DNA surrounding the SNP location and blasting the DNA using blastx against the amino acid sequences of the reference strain. If the match is not 100 % you have a non-synonymous SNP
If you have a variant call file from your WGS analysis, you can easily use SNPeff against your reference genome of interest. See http://snpeff.sourceforge.net/
The original Nei-Gojobori method could be of use to you Arzuba; it does not require any phylogenetic information, only aligned codon sequences. I would however caution you in that there is an error in their calculation of variance (from their '94 paper) that tends to underestimate positive selection the larger a gene gets. While this method is a few decades old, there are still plenty of recent publications that make use of it.
DataMonkey is the best online server who can help you to find synonymous and nonsynonymous sites of the genome, but first you must split the genome in codon sequences.
there is no simple way, and I would suggest you follow Aldert's suggestions. But first you should identify a reference strain/species and have it amino acids sequence around those SNP site in hand, then simple alignment across all strains will give you the answer.
Would you be able to clarify the goal of identifying synonymous and nonsynonymous sites in your sequences, or do you mean identifying synonymous and nonsynonymous substitutions? Also, why does the low number of SNPs make using PAML difficult; you can use the 1x4 frequencies with the GY94 model if you don't have enough variation to estimate the 3x4 or 61x61 frequencies.
If you want to know synonymous and nonsynonymous substitutions only, you can write a simple perl or python script to count them between pairs of species and print out a list of which sites they are. Doing this for a tree is a little trickier, but it can be done.
There really is not a way to find out what the synonymous and nonsynonymous sites are, as this is really dependent upon the substitution pathway and why estimators of dN and dS average or weight between them.
Does this help, or is your intent to test for selection across the rickettsia strains? There are lots of interesting test you can perform such as detecting selective sweeps, identifying shifts in selective pressures, or testing for sites under positive selection.
I have done a similar approach
Where I had to find selected genes among Same species but different strains.
If you are interested you can read it here
In addition, MAGA has such option to indentify site wise substitution rate.
Article Identification of the positively selected genes governing ho...
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