Question: Phylogeny Analysis Data
2
gravatar for l.souza
23 months ago by
l.souza70
Brasilia, Brazil
l.souza70 wrote:

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?

ADD COMMENTlink modified 23 months ago by genebow150 • written 23 months ago by l.souza70
2

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)

ADD REPLYlink written 23 months ago by cpad011211k
1

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.

ADD REPLYlink modified 23 months ago • written 23 months ago by Michael Dondrup46k

Perhaps many isolates of a virus?

ADD REPLYlink written 23 months ago by genomax67k

I edited the post...

ADD REPLYlink written 23 months ago by l.souza70

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

ADD REPLYlink written 23 months ago by h.mon25k

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

ADD REPLYlink written 23 months ago by l.souza70
2
gravatar for genebow
23 months ago by
genebow150
USA/Chicago
genebow150 wrote:

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

ADD COMMENTlink written 23 months ago by genebow150
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