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.auhttp://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
