estwise is a part of the Wise2 package that focuses o�n comparisons of biopolymers

Wise2 is a package focused o�n comparisons of biopolymers, commonly DNA sequence and protein sequence. 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.

The main programs within Wise2 are:-
genewise compares a protein sequence or a protein profile HMM to a dna sequence.
genewisedb is the database searching version of genewise. It takes a database of proteins and compares it to a database of dna sequences (genewisedb - search modes).
estwise runs very much like genewise with basically a subset of options. For completeness they are all listed below (estwise - options: dna/protein).
estwisedb is the database searching version of the estwise program. Like estwise, it has the same sort of running modes as genewisedb, but with more limited options.

These programmes all have basically the same running mode:-

%genewise protein-file dna-file

Other programs:-
dba - standing for Dna Block Aligner, was developed by Niclas Jareborg, Richard Durbin and Ewan Birney for characterising shared regulatory regions of genomic DNA, either in upstream regions or introns of genes.
psw - a short and sweet program for calculating smith waterman alignments quickly. It was mainly written as C driver to test the underlying code which is more useful in things like the Perl port.
pswdb - protein smith waterman database searching was written by Richard Copley using the underlying Wise2 libraries psw - options.

A number of options are common to these programs from the point of view of how they run:

• - help
  verbose help of all options.
• - version
  show version and compile info.
• - silent
  No messages o�n stderr, whether reports or warnings.
• - quiet
  No reports or information messages o�n stderr.
• - erroroffstd
  No warning messages to stderr, but reports are still issued.
• - errorlog
  [file] Log warning messages to file.