MrBayes question

Karol Marhold karol.marhold at SAVBA.SK
Fri Sep 9 11:15:04 CDT 2005


Dear all,
I wonder if somebody here could help us with the following
problem related to the use of the program MrBayes:
Using command "sumt" with the option "saveblens=yes" we receive
a consensus tree in the file .con. When this tree is opened in
TreeView there is a possiblity to get the tree with unequal or equal
branch lengths. We understand that unequal tree branches reflect
sequence divergence, but we are not sure exactly in which way this
divergence is expressed (i.e. how branch lengths are computed) as
this is in fact consensus tree. In the paper by Lin et al., Syst.
Biol. 53: 400-421, 2004, the authors use the following formulation:
"branch lengths are optimised using estimated mean parameter value
and drawn proportional to character change as indicated by the scale
bar". We wonder if this is correct and we also wonder how it is possible
that for identical sequences we obtained slightly different branch
lengths.


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Karol Marhold
Institute of Botany, Slovak Academy of Sciences
Dubravska cesta 14, SK-845 23 Bratislava, Slovak Republic
Tel.: (+421) 2 5942 6128  Fax: (+421) 2 5477 1948
E-mail: karol.marhold at savba.sk
http://ibot.sav.sk/Karol01.html
see also http://www.iopb.org
and have a look to the prototype of our database
on chromosome numbers http://147.213.100.121/webapp/
&
Department of Botany, Charles University,
Benatska 2, CZ-128 01 Praha, Czech Republic
Fax: (+420) 2 2195  1645

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