Hi,
this message was recently posted on EvolDir. Maybe you'll find it
interesting.
Rgds, Ari
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The program SOAP (version 1.0) is now available to alpha testers at
http://dbm.ulb.ac.be/ueg/SOAPdoc.html
SOAP stands for "Stability Of Aligned Positions" and it can be used
for exploring the stability of multiple sequence alignments to
variations in parameters such as gap opening/extension penalties or
taxon sampling.
Indeed, different sites in nucleic-acid and amino-acid sequences can
evolve at very different rates such that the efficiency with which
homology is inferred across taxa/sequences can greatly vary,
depending both on the block of sites considered and alignment
parameters used (see for example Vingron & Waterman 1994).
Furthermore, different alignments produced through the use of
different heuristic alignment parameters can yield significantly
different results when subjected to phylogenetic analyses. SOAP is
based on a conservative approach assuming that confidence in homology
assessment within a column of aligned characters increases with
stability of this assessment to perturbation of alignment parameters.
SOAP is a simple and user-friendly program that can be used to
produce and compare CLUSTALW alignments. Unstable positions are
automatically indicated and can be removed when exporting the
alignment (in 'Nexus', 'NBRF/PIR', 'Molphy', 'Phylip', or 'Text'
formats).
PROGRAM AVAILABILITY.
SOAP is mostly written in Java. Stand-alone versions are available
for Linux, MS Win32 and MacOS (ppc). We can also provide a version of
SOAP allowing to send the alignment tasks to a UNIX-like server. We
are currently developing a version of SOAP allowing the tasks to be
distributed on multiple processors.
The alpha version of SOAP seems to be reasonably stable. If you would
like to participate on testing SOAP, please visit the web page
(http://dbm.ulb.ac.be/ueg/SOAPdoc.html) or send an e-mail to Ari
Loytynoja (apl at dbm.ulb.ac.be). SOAP is distributed free of charges.
Have fun, Michel.
Ref:
Vingron M. & M. S. Waterman 1994. Sequence Alignments and Penalty
Choice. Review of Concepts, Case Studies and Implications. J. Mol.
Biol. 235:1-12.
----------------------------------------------------
Michel C. Milinkovitch,
Associate Professor,
Unit of Evolutionary genetics,
Inst. of Molecular Biology & Medicine,
Free University of Brussels (ULB),
cp 300,
Rue Jeener & Brachet, 12,
B-6041 Gosselies, Belgium.
Tel: +32-2-650-9956 (my office),
+32-2-650-9967 or 9968 (lab),
+32-2-650-9952 or 9953 (students)
Fax: +32-2-650-9950;
e-mail: mcmilink at ulb.ac.be
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