Contents of this distribution

==============================================
Files with information about this distribution
==============================================
CONTENTS          -- this file
COPYING           -- license info for Lamarc and third party tools we 
                       distribute
HISTORY           -- major Lamarc project versions/milestones
INSTALL           -- a pointer to doc/html/compiling.html (installation 
                       instructions)
README            -- overview of Lamarc project and distributions available

======================================
Files used or created by the autotools
======================================
Makefile.am       -- Automake makefile for the entire project
Makefile.in       -- generated from Makefile.am by automake, 
aclocal.m4        -- aclocal generates this
configure.ac      -- autoconf generates configure from this
configure         -- generates Makefile from Makefile.in

config/           -- helper scripts and files used or generated by ./configure
                     including conf.h

depcomp           -- belongs in config/ directory but awaiting autotools bugfix
install-sh        -- belongs in config/ directory but awaiting autotools bugfix
missing           -- belongs in config/ directory but awaiting autotools bugfix

=============================
Lamarc Code and Documentation
=============================
doc/              -- documentation directory
doc/html          -- HTML documentation
doc/licenses/     -- complete text of licences for all software in this distribution
doc/testfiles     -- program test files
resources/        -- icons and packaging support
src/bayeslike     -- code specific to doing Bayesian search
src/control       -- the main control routines of LAMARC
src/convErr       -- error handling for converter gui
src/conversion    -- legacy file conversion program
src/convModel     -- gui-free parts of data storage for converter gui
src/convParse     -- parsing related structures for converter gui
src/convStrings   -- error messages and dialog strings for converter gui
src/convUtil      -- utility methods for converter gui
src/datalike      -- routines dealing with data and data likelihoods
src/force         -- code for different evolutionary forces (e.g. migration)
src/guiconv       -- gui-involved parts of converter gui
src/guiutil       -- gui stuff thought to be generally useful
src/lamarcmenus   -- lamarc-specific menus
src/menu          -- general-purpose menu routines
src/postlike      -- posterior-likelihood computation and display routines
src/report        -- output reporting
src/tools         -- utility routines (string handling, random numbers, etc.)
src/tree          -- phylogenetic trees and rearrangement
src/ui_interface  -- non-menu parts of lamarc's UI
src/ui_util       -- utilities used by UI (e.g. undo/redo machinery)
src/ui_vars       -- storage of settings data during user input
src/xml           -- input data handling in XML

================================================================
Third-party tools -- see COPYING file for licenses and more info
================================================================
boost/            -- highly useful C++ library collection
tinyxml/          -- bare-bones xml parser 
wxWidgets/        -- multi-platform GUI library
wxWidgetsLamarc/  -- (may be empty) Lamarc patches to wxWidgets library


$Id: CONTENTS,v 1.5 2007/09/17 20:39:53 lpsmith Exp $