Question: Transcript or cds for phylogenetic tree ?
0
gravatar for Picasa
8 days ago by
Picasa530
Picasa530 wrote:

Hi,

I would like to make a single phylogenetic tree after a multiple alignment of sequences of differents species.

For the sequences, should I use the whole transcript or only de CDS part ? or it doesn't matter.

Thanks for your help.

msa phylogenetic • 63 views
ADD COMMENTlink modified 8 days ago by lieven.sterck7.8k • written 8 days ago by Picasa530
3
gravatar for lieven.sterck
8 days ago by
lieven.sterck7.8k
VIB, Ghent, Belgium
lieven.sterck7.8k wrote:

It does matter.

Go for the CDS (or the protein is even better). Evolutionary constraints/conservation works mainly on those sequences (and less on the UTR, which is what you add when using the complete mRNA/transcripts).

If in the unlikely event that the CDS/protein does not give you enough 'resolution' you might consider adding UTRs to the analysis but keep in mind that comes with a whole bunch of other issues :/ (you might even go very wild and add all the introns, but let's no go there yet :) )

ADD COMMENTlink written 8 days ago by lieven.sterck7.8k

Thanks for your answer.

Evolutionary constraints/conservation works mainly on those sequences

I am not sure to understand this. Do you mean algorithm used by phylogenetic softwares (such as raxml or phyml or whatever) used model that worked with cds (dna level) and/or amino acid ?

ADD REPLYlink modified 8 days ago • written 8 days ago by Picasa530

well, yes and no.

I meant that the biological constraints put into place by evolution mainly play on those kind of sequences. As a consequence the algorithms that model/analyse those things are also best performing (optimised) on those sequences indeed.

ADD REPLYlink written 8 days ago by lieven.sterck7.8k
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