MrBayes and mtrev

Thomas Buckley BuckleyT at landcareresearch.co.nz
Tue Mar 25 20:34:09 EST 2003


Hi,

You can get the mtREV24 matrix from PAML.  The file is called mtREV24.dat.  I'm not aware that anyone is updating the matrix as new sequences become available, but its probably time that someone did given the large number of complete mtDNA genomes now available.

I don't know of any model specifically for invertebrates.  Most people seem to use mtREV24, which may not be appropriate.

Thomas

Thomas Buckley
Landcare Research
Private Bag 92170
Auckland
New Zealand

E-mail:BuckleyT at LandcareResearch.co.nz
Phone: +64-9-8154200 x 7084
Fax: +64-9-8497093

>>> Mark Dowton <mdowton at uow.edu.au> 26-Mar-03 1:59:41 PM >>>
We're doing some phylogenetic analyses based on mt amino acid sequences,
and for consistency I would like to align the sequences with Clustal
using a mtrev model to estimate distances (rather than Blosum or PAM,
which are based on nuclear genes), then use aamodel=mtrev in the
subsequent MrBayes analysis.  Can anyone point me to the most recent
mtrev step matrix (the most recent version is mtrev24, I think)? and
does anyone know how to examine precisely the mtrev model that MrBayes
uses?

On a related note, as I understand it, these mtrev models are based on
alignments of vertebrate mt genomes, excluding one mt protein due to it
being coded on a different mt strand.  The mtrev model has been adopted
more generally for mt amino acid alignment comparisons generally (ie
outside of the vertebrates).  Have there been mtrev models generated for
non-vertebrate groups?

--
Mark Dowton
Institute for Conservation Biology
Dept Biology
Wollongong University
Wollongong  NSW  2522
AUSTRALIA
Phone: 61-2-42215479
Fax: 61-2-42214135
mailto:mdowton at uow.edu.au
http://www.uow.edu.au/science/biol/staff/mdowton/markdowton.html

And

Centre for Evolutionary Biology & Biodiversity
Dept Evironmental Biology
Darling Building
Adelaide University  SA  5005
AUSTRALIA

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