Question: Phylogeny Analysis Data
2
gravatar for l.souza
3.0 years 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 3.0 years ago by genebow160 • written 3.0 years 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 3.0 years ago by cpad011213k
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 3.0 years ago • written 3.0 years ago by Michael Dondrup47k

Perhaps many isolates of a virus?

ADD REPLYlink written 3.0 years ago by genomax84k

I edited the post...

ADD REPLYlink written 3.0 years ago by l.souza70

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

ADD REPLYlink written 3.0 years ago by h.mon29k

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

ADD REPLYlink written 3.0 years ago by l.souza70
2
gravatar for genebow
3.0 years ago by
genebow160
USA/Chicago
genebow160 wrote:

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

ADD COMMENTlink written 3.0 years ago by genebow160
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2169 users visited in the last hour