[Taxacom] base alignment

[Jaakko Hyvönen]

Dear John, as a suitable entry to this topic I would recommend the following:

Wheeler, W. C. 2005. "Alignment, Dynamic 
Homology, and Optimization." pp71-80 in 
Parsimony, Phylogeny, and Genomics. V. A. Albert 
eds. Oxford University Press, Oxford.

or the older article:

Phillips, A., D. Janies, and W. C. Wheeler. 2000. 
"Multiple sequence alignment in phylogenetic 
analysis." Mol. Phyl. Evol. 16:317-330.

if you don´t have access to these publications 
you can download them in pdf-format from Ward 
Wheeler´s homepage 
http://research.amnh.org/scicomp/ward_wheeler.html

there you will find also many other articles (and software) about this topic

hope this helps, all the best, jaakko

>I would be interested in any feedback or direction to suitable
>publications or web sites that outline the procedures by which
>substitutions and gaps are balanced to result in base alignments between
>species. In my current (and perhaps primitive) understanding, this
>process does not appear to be cladistic, but a theoretical model by
>which homologies are constructed. If this understanding is correct (and
>so some of you may point out that it is not) it would seem to me that
>character states in molecular studies are not empirical in the same way
>that they are in morphology (i.e. the homologies are the result of a
>calculation in molecular studies).
>
>John
>
>Dr. John R. Grehan
>Director of Science and Collections
>Buffalo Museum of Science1020 Humboldt Parkway
>Buffalo, NY 14211-1193
>email: jgrehan at sciencebuff.org

-- 
Jaakko Hyvönen 
Plant Biology (Biocenter 3), PO Box 65, FIN-00014 UNIV. HELSINKI, FINLAND

e-mail      jaakko.hyvonen at helsinki.fi
phone cell +358-(0)50-5171184
facsimile  +358-(0)9-19157788

http://www.helsinki.fi/~jhyvonen
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