Phylogeny Analysis Data

Question

[l.souza]

I have nucleotide and amino acid sequences of 7 sorotypes of a virus (they differ into two divergent groups that are internally close related). What of these is best kind of data for inferring phylogenetic trees?

[cpad0112]

Assuming that you have 7 serotypes of a virus, DNA sequences must be highly conserved. One can use alignment (sequence) to arrive at phylogenetic distances and tree. But one needs to use appropriate matrix. Choose an alignment matrix that is good for highly conserved alignment. For eg in aligning highly conserved protein sequences, people use higher blosum matrix (blosum 80) and for sequences with low conservation, people use lower numbered blosum matrix (blosum 20 or so)

[Michael]

sequences of a virus, What of these ...

None! You have a single species. If you want to generate a phylogeny, you need to find orthologues in other viruses first.

[GenoMax]

Perhaps many isolates of a virus?

[l.souza]

I edited the post...

[h.mon]

Seven closely related sorotypes? Seven distantly related, divergent sorotypes?

[l.souza]

Four of them are closely related while the other three are more distant.

Answer 1

[Charles Yin]

You may use whole DNA or RNA sequences of the virus genomes for phylogenetic analysis.