wise-doc 2.4.0-1 (i386 binary) in ubuntu gutsy

 Wise2 is a package focused on comparisons of biopolymers, commonly DNA
 and protein sequences. There are many other packages which do
 this, probably the best known being BLAST package (from NCBI) and the
 Fasta package (from Bill Pearson). There are other packages, such as
 the HMMER package (Sean Eddy) or SAM package (UC Santa Cruz) focused
 on hidden Markov models (HMMs) of biopolymers.
 .
 Wise2's particular forte is the comparison of DNA sequence at the level
 of its protein translation. This comparison allows the simultaneous
 prediction of say gene structure with homology based alignment. There is
 currently no other package that I know of that contains this type of
 algorithm with a full blown gene prediction model and a hidden Markov
 model of a protein domain.
 .
 Wise2 also contains other algorithms, such as the venerable Smith-Waterman
 algorithm, or more modern ones such as Stephen Altschul's generalised
 gap penalties, or even experimental ones developed in house, such as
 dba. The development of these algorithms is due to the ease of developing
 such algorithms in the enviroment used by Wise2.
 .
 Wise2 has also been written with an eye for reuse and maintainability.
 Although it is a pure C package you can access its functionality
 directly in Perl. Parts of the package (or the entire package) can
 be used by other C or C++ programs without namespace clashes as all
 externally linked variables have the unique identifier Wise2 prepended.
 Java and CORBA ports are being considered - see the API section
 .
 Finally Wise2, although implemented in C makes heavy use of the Dynamite
 code generating language. Dynamite was written for this project, by
 Ewan Birney. There is a separate documentation for Dynamite found at
 http://www.sanger.ac.uk/Software/Dynamite.