File	Date	Author	Commit
benchmarks	2016-03-03	jmricher	[fef70b] Initial commit v3.1
bin	2016-03-03	jmricher	[fef70b] Initial commit v3.1
build	2016-03-03	jmricher	[f41779] genetic algorithm + sampars
config	2016-03-03	jmricher	[fef70b] Initial commit v3.1
include	2016-03-03	jmricher	[f41779] genetic algorithm + sampars
src	2016-03-03	jmricher	[f41779] genetic algorithm + sampars
tests	2016-03-03	jmricher	[fef70b] Initial commit v3.1
.cproject	2016-03-03	jmricher	[fef70b] Initial commit v3.1
.project	2016-03-03	jmricher	[fef70b] Initial commit v3.1
INSTALL	2016-03-03	jmricher	[fef70b] Initial commit v3.1
README	2016-03-03	jmricher	[fef70b] Initial commit v3.1
intel.txt	2016-03-03	jmricher	[fef70b] Initial commit v3.1
m1038.txt	2016-03-03	jmricher	[fef70b] Initial commit v3.1
makefile	2016-03-03	jmricher	[fef70b] Initial commit v3.1
seeds.txt	2016-03-03	jmricher	[fef70b] Initial commit v3.1
sets.txt	2016-03-03	jmricher	[fef70b] Initial commit v3.1
taskset.txt	2016-03-03	jmricher	[fef70b] Initial commit v3.1
times.txt	2016-03-03	jmricher	[fef70b] Initial commit v3.1

Read Me

=====================================================================
Standard Bioinformatics Library v3.1 and higher
=====================================================================
Copyright 2009-2015 Jean-Michel Richer
email: jean-michel.richer@univ-angers.fr
http://www.info.univ-angers.fr/pub/richer
=====================================================================


=====================================================================
	SBL 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.

    SBL 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 SBL.  If not, see <http://www.gnu.org/licenses/>. 
 =====================================================================
    
See the INSTALL file for more information on how to install the SBL package.    

See the BUILD file for more information on how to compile source files and
build the library and programs.


Release Note:

- Phylip file format is not supported because it is ambiguous, please
use the program "readseq" under Linux to convert Phylip files to Fasta or 
MSF file format, or use the "sequence group" file format which is simpler.

- "sequence group" file format is very simple, each non empty line represents
a sequence, which starts by the name of the sequence and then the residues.
Blank characters (space, tabulation) represent the separators between the
sequence name and the residues. Here are some examples :

human_2		ACGTGTGATGGT---AGGTGATGGAG	AGTGTGGTT--GGG GGAGAGG
gorilla AGTGTGQGTGGGTG?TAGGTATA---GTGGAGTGA

- MSF and Nexus file formats are supported

Phylip file format

There are many Phylip file format, we allow only one file format as follows
[possible spaces][number of taxa][spaces][taxa length]
[name of sequence 1][spaces][residues with no space]
...
[name of sequence n][spaces][residues with no space]
[possible spaces][residues of sequence 1 with no space]
...
[possible spaces][residues of sequence n with no space]
...

here is an example:
  3 10
my_sequence_with_a_very_long_name AAAAA
short_one                      CCCC
last_one GGG
 AAAAA  
CCCCC
    GGGGGG

modify the file config/config.params
type 'make config' in a terminal
To generate release : make release
To generate debug   : make debug
To generate tests for release distribution : make tests_release
To generate tests for debug distribution : make tests_debug