Hi, All
Recently I want to construct the phylogenetic tree, but i did not want the branch length is measured in evolutionary distance, but measured in number of SNPs. which software or method can be used for this? thanks for help.
It sounds like you're interested in dS/dN ratios. You could try this approach. Then, you could build a tree based on those values. I don't like this way to view the data because a tree depicts relationships and the dS/dN values may not be related to each other for different taxa (sequences) that show a join on the tree. Why not just show this information as a bar graph? You could group genes or sort genes by dS/dN values, or by GO (ontology) terms, or chromosomal position, or anything else.
There are a few ways to measure distance, one is the number of nucleotide (or amino acid) differences between each pair of a set of sequences. Which is what it sounds like you're asking for.
I like the PHYLIP suite to do this kind of work, but you might find it difficult to use if you're not used to command line programs. To make a distance tree in Phylip, put your multiple sequence alignment into either protdist or dnadist, then plug the output (a matrix of the # of differences between sequences) into neighbor which will give you a tree.
I like figtree for making a nice tree from that output.
If this is too elementary for you, pardon me, it's hard to tell your level of expertise from your question.
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As a point of clarification are you building a tree of individuals? If you are building a tree of organisms than you aren't talking about SNPs any more but fixed mutations between species.
+1 You do need to clarify the taxonomic levels you're working on. Are you building haplotype trees or networks? Usually those analyses use SNPs.