readme.txt

SPAGeDi: Spatial Pattern Analysis of Genetic Diversity

Copyright (c) 2002-2009 Olivier Hardy (ohardy@ulb.ac.be) and Xavier Vekemans
  
Portable/Unix source code maintained by Reed A. Cartwright (cartwright@asu.edu).

Website: <http://ebe.ulb.ac.be/ebe/SPAGeDi.html>
GitHub: <https://github.com/reedacartwright/spagedi>
Downloads: <http://scit.us/spagedi/>

LICENSE

  This program is free software: you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation, either version 3 of the License, or
  (at your option) any later version.

  This program is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with this program.  If not, see <http://www.gnu.org/licenses/>.

CITATION

Hardy, O. J. & X. Vekemans (2002). SPAGeDi: a versatile computer program to
analyse spatial genetic structure at the individual or population levels.
Molecular Ecology Notes 2: 618-620.

URL: http://iee.ulb.ac.be/sciences/lagev/fichiers/Spagedi_MENotes2002.pdf

NOTA BENE

SPAGeDi has been tested on several data sets and results were checked for con-
sistency with alternative softwares whenever possible. It may nevertheless still
contain bugs (corrected bugs are listed at the end of this manual). Some of
these bugs are probably easy to detect by causing the program to crash or lead-
ing to obvious erroneous results for particular data sets and analyses. But
others, more critical, may just cause biased results that appear plausible.
Hence, it is advised to take much care checking the consistency of the infor-
mation from the results file. The authors would appreciate being informed of any
detected bug. The authors claim no responsibility if or whenever a bug causes a
misinterpretation of the results given by SPAGeDi.

USING SPAGEDI

See manual.pdf for detailed instructions on using SPAGeDi.

DOWNLOADING AND INSTALLING

Binary packages for SPAGeDi can be downloaded from <http://scit.us/spagedi/>.

COMPILING FROM SOURCE CODE

SPAGeDi requires CMake 2.8 (<http://www.cmake.org/>) to build it from sources.
Many Unix-like operating systems can install CMake through their package
systems.

Download the SPAGeDi source code (<http://scit.us/spagedi/>) and issue the
following commands:

	tar xvzf SPAGeDi-.*.tar.bz2
	cd SPAGeDi-.*/build
	cmake ..
	make
	make install

You may have to adjust the first two commands to fit the archive that you
download.

The '-G' option to cmake is used to specify different build systems, e.g. Unix
Makefiles versus KDevelop3 project.  The '-D' option to cmake can be used to set
different cmake variables from the command line:

	cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr .
	make
	make install

This will build an optimized version of SPAGeDi and install it to '/usr/bin'. To
specify your own build flags you need to set the environment variables CFLAGS
and LDFLAGS as neccessary.  Then specify

	cmake -DCMAKE_BUILD_TYPE= .

See CMake's manual for additional information.