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SOAP 1.0 released

apl at dbm.ulb.ac.be apl at dbm.ulb.ac.be
Fri Nov 17 06:58:54 EST 2000


Hi,
this message was recently posted on EvolDir. Maybe you'll find it
interesting.

Rgds, Ari
---

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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