Phylogeny Analysis Data
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?
• 2,473 views
•
link
updated
by
Charles Yin
•
written
by
l.souza
•
written
by
l.souza
1 answer
You may use whole DNA or RNA sequences of the virus genomes for phylogenetic analysis.
• 0 views
•
link
written
by
Charles Yin
Log in to answer this question.
More posts like this
-
Parameter setting in BEASTv2.6.7
written by wes •
-
Compare protein functionality between species
written by Howard •
-
Plylogenetic tree construction
written by majeedaasim •
-
How many sequences to phylogeny?
written by l.souza
-
Multiple Alignment (~1400 sequences)
written by l.souza
-
chi squared test for comparing two groups of proteins
written by Sudheer Gupta •
-
Effect of indel mutation on protein
written by sahar.ava •
-
how to extract blastxed sequences' corresponding amino acid sequences
written by Kurban
-
Conservation At Amino Acid Level
written by Biomed
-
How To Set The Substitution Model In Phyml?
written by Dejian
None! You have a single species. If you want to generate a phylogeny, you need to find orthologues in other viruses first.
Perhaps many isolates of a virus?
I edited the post...
Seven closely related sorotypes? Seven distantly related, divergent sorotypes?
Four of them are closely related while the other three are more distant.
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)