Hi all -
In Message-Id: <9306231808.AA00773 at net.bio.net> ahouse at hydra.rose.brandeis.edu
(Jeremy John Ahouse) describes a problem that I have been complaining about for
years. Since it makes so much more biological sense to align amino acids...
> I have done a series of multiple alignments. The alignments were done
>with inferred amino acid sequences. Now that I am happy with the
>alignments I want to go back to the mRNA sequence (which I have) for some
>of the clustering and parsimony analysis. I want to enforce the alignments
>(gaps, etc...) from the aa's on the nucleotide alignment.
>> I know I can do this by hand, but are there any tools that help with
>this, that you all know about?
To date I am aware of two programs which can automate this problem:
1) Doug Eernisse's (Doug_Ee at um.cc.umich.edu) Mac-based HyperCard Stacks "DNA
Translator and Aligner" have this capability.
2) Joe Felsenstein's PHYLIP package (ftp to evolution.genetics.washington.edu)
now (version 3.5) has an unsupported program named MakeInF which supposedly
also can perform the dirty deed.
I have NOT used either of these programs, so I can not attest to how well they
work. Another point to consider is the new PHYLIP as well as still having
ProtPars for protein parsimony analysis now has the program ProtDist to allow
the use of Distance method algorithms with protein data. I HAVE used this
approach and it works great!
Hope this helps, Steve
Steven M. Thompson
Consultant in Molecular Genetics and Sequence Analysis
VADMS (Visualization, Analysis & Design in the Molecular Sciences) Laboratory
Washington State University, Pullman, WA 99164-1224, USA
AT&Tnet: (509) 335-0533 or 335-3179 FAX: (509) 335-0540
BITnet: THOMPSON at WSUVMS1 or STEVET at WSUVM1
INTERnet: THOMPSON at wsuvms1.csc.wsu.edu
