Lamarc 2.1.10
Sep 3 2014
===============

A program to estimate population parameters from genetic data.  All
parameters are estimated jointly.  Currently the program allows estimation
of population sizes, recombination rate, migration rates, growth
rates, and population divergence times, and can estimate the location of 
a trait allele.

This version is a bug fix update to version 2.1.8 (May 2012).  It
fixes severe bugs in estimation of divergence times and of migration
in the presence of divergence; runs inferring those parameters should
be re-done.  The bugs did not exist prior to 2.1.8 as divergence was
not released before that.

DOCUMENTATION & GETTING HELP
============================

Extensive documentation is available in the doc/ subdirectory of
your lamarc distribution.  You will likely wish to begin with
the HTML documentation available in doc/html/index.html .

Careful reading of the documentation will be necessary to obtain
a high quality lamarc analysis of your data.  As the program user,
you will need to make decisions such as
    * which evolutionary forces to model,
    * which mutational model to assume for your data, and
    * how long to run the program.
Please note that there may be specific documentation sections
relevant to your particular data type, such as viral data, or
phase unresolved data.

The most up-to-date information on Lamarc is available at the project
website http://evolution.gs.washington.edu/lamarc/

If, after reading the relevant documentation, you still have questions,
please email the lamarc developers at:

    lamarc@uw.edu

BINARY DISTRIBUTIONS:
=====================
If you have downloaded a binary distribution (executables) you are all 
set and the programs "lamarc" and "lam_conv" are in the same directory 
as this README.

Linux users--you may recieve a cryptic sounding error message concerning
"libstdc++.so.6" or something similar.  In order to run lamarc you
will need to either get the lamarc source distribution and compile
it on your computer, or you will need to install some variant of
version 6 of the standard c++ shared library.  Debian users with
"apt" installed can use "apt-get install libstdc++6" to get the needed
library.

SOURCE DISTRIBUTIONS:
=====================
If you have downloaded the source and have a *UNIX* system (LINUX,
BSD, MACOSX, SOLARIS, TRU64, etc) see doc/html/compiling.html for
directions to build "lamarc" and "lam_conv".

