have 127 fasta sequences from RNA virus from 6 different genotypes and 2 different subtypes from 2008 to 2010.I want to demonstrate its divergence along time (between the references sequences and my set) and divergence to each other. How to Graphycally represent it?
Note:I have an big similarity matrix from my sequences(pairwise distance) with p-distance values.
Viral phylogenies are somewhat tricky, because there isn't a single gene that is conserved amongst all different groups of viruses. For RNA viruses, there should be at least RNA-dependent RNA polymerase and possibly others in your dataset. So I would try to detect all 1-to-1 orthologs in your dataset that are represented in your dataset and do phylogenetic reconstruction on them. How this analysis is best done depends on how similar the virus sequences are overall. This might include whole genome alignments or concatenated alignments of orthologs or single gene or protein alignments that are condensed into a consensus tree.
The matrix you made, can be useful to detect orthologs if it is based on individual genes, however it is not useful for doing phylogeny.
probably viral coat proteins