Hi,
I'd like to know what difference makes using FULL PROTEIN SEQUENCES versus PROTEIN CONSERVED DOMAIN SEQUENCES in order to make a phylogenetic tree.
In my case, the goal is to put in phylogenetic context hallmark genes of newly discovered virus sequences.
Thank you,
Guillermo
If you have complete sequence, I would recommend to use full sequence.
Conserved sequences have phylogenetic data on deep changes among the sequences. Protein coding sequences can suffer from convergent evolution but generally are excellent for sorting out selection dynamics.
It really depends on how distantly related are the organisms you are analyzing.
Conserved domains, as the name suggests, tend to be less variable over time and they would be not useful if you want to construct a phylogeny of closely related organisms but could be useful if the organisms are distantly related.
My suggestion, according to your goal, would be to use the full sequence (i strongly suggest using the CDS if you have it instead of the aminoacid sequence), align and manually curate the multiple alignment.
Gustavo Rodriguez Alonso and Patrice Showers Corneli THANK YOU SO MUCH FOR YOUR ANSWERS!
I am studying ssDNA and RNA viruses, so my viral sequences are expected to share low degree of similarity given the faster evolutionary rates for these viruses.
How do I curate an alignment for that? Is it just a matter of trimming - removing all sequence portions that are not the conserved domains?
THANK YOU
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