These directories have the source code for the
Wise2 package and the Dynamite compiler. The 
directories are as follows.



base      - base memory, string and error reporting library

dynlibsrc - bioinformatics library - sequences, genes, codon tables
            etc

models    - algorithms and more complex objects for the wise2 package

dyc       - dynamite compiler source code.

HMMer2    - the HMMer2 package - used for hmmio in this case
	The source code here was provided by Sean Eddy <eddy@wol.wustl.edu>

perl      - Integration into perl via an XS interface: makefile for the interface

perl/Wise2 - the actual Perl 'directory' to compiled for it

perl/Wise2/libs - where the libraries are copied into to build perl

examples  - examples for the Wise2 package

dynamite_examples - examples for the Dynamite package.



Source code files:

	There is a scary number of files in each directory. This is
because the dynamite compiler generates alot files for each module
here is an explanation of the files

	.dy - the dynamite source

For each .dy files the following files are generated

	.h - C header file - contains documentation
	.c - C source file
	_api.t api 'type' file
	_api.h api header file
	.pod - pod documentation
	.xs - xs interface into perl



More documentation occurs in a appropiate file. Read the .h  files for
each module

base library
	wisestring - common string functions
	wisememman - memory management
	wiseerror  - error functions
	wisetime   - (small) time functions
	wiserandom - wrapper around random functions
	wiseconfig - almost defunct configuration

dynlibsrc

	Sequence types

	sequence - base sequence object
	protein - typed protein sequence object
	genomic - typed genomic sequence object
	cdna	- typed cdna object

	Sequence databases

	sequencedb - sequence database
	proteindb - protein database
	cdnadb - cdna database
	genomicdb - genomic database
	randommodel     - protein+dna random models

	Central dogma types

	genomicregion - holder for gene structures on a genomic sequence
	gene - gene structure 
	transcript - one transcript from a gene 
	translation - one translation from a transcript

	Sequence accessories

	codon - codon table, base encoding and translation
	compmat - protein comparison matrix
	dnamat - dna comparison matrix
	codonmatrix - codon comparison matrix

	Dynamic programming libraries

	basematrix - underlying memory of DPs
	dpenvelope - a envelope over the dynamic programming
	packaln - low level alignment
	aln - high level alignment
	

	Alignment Output libraries

	asciibtcanvas - ascii class for outputs
	btcanvas - virtual class for outputs


	Database searching accessories

	hscore - high scores
	histogram - package for handling score distributions (from sean eddy)
	database.h - generic types for database looping	

Models

	Protein<->protein alignmetns

	proteinsw.dy  - smith waterman protein alignments
	abc.dy        - stephen altschul's 'generalised' gap penalties
	sw_wrap.dy    - a clean API for the protein smith waterman

	HMM support

	wise2xhmmer2    - conversion from hmmer<->wise
	threestatemodel - internal wise2 profile-HMM object
	threestatedb    - database of HMMs
	pfamhmmer1db    - old-style HMM 1.x db (driectory)- new style done by wise2xhmmer2

	GeneWise/EstWise algorithm support

	genewisemodel - extended HMM for genewise/estwise
	geneparameter - raw frequencies for gene model
	geneparser21  - probability model for 21:93
	geneparser4   - probability model for 6/4 state models
	splicesitemodeler - splice site models
	
	GeneWise algorithms

	genewise4 - 421 algorithm
	genewise6 - 623 algorithm
	genewise21 - 2193 algorithm
	geneloop6 - 623 looping algorithm
	geneloop21 - 2193 looping algorithm
	
	EstWise algorithms
	
	estwise3 - 333 algorithm
	estloop3 - 333 looping algorithm
	estfrag3 - [not used] est fragment
	estslim3 - 312 algorithm
	
	Clean api into package

	gwrap - genewise algorithm API
	estwrap - estwise algorithm API

	dba support

	dba - dba algorithm

Executable main functions

	genewise.c - genewise 
	genewisedb.c
	estwise.c
	estwisedb.c
	psw - protein smith waterman
	dbac.c - dba calling function