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File Date Author Commit
 analysis 2016-12-09 grabherr [r43] Changed default for iterations.
 base 2016-11-03 grabherr [r42] Removed -ggdb3 and bounds checking.
 math 2013-05-30 grabherr [r10] Include the math directory to fix build problem.
 simulation 2013-04-22 grabherr [r8] Added simulation directory.
 system 2011-06-30 grabherr [r1] Initial check-in.
 test_data 2014-11-29 grabherr [r27] Add chromosome painting tool.
 util 2016-06-29 grabherr [r39] Added parameter maxNA.
 visual 2016-08-18 grabherr [r41] Update to the latest version.
 LICENSE 2011-06-30 grabherr [r1] Initial check-in.
 MakeDepend.cc 2011-06-30 grabherr [r1] Initial check-in.
 Makefile 2011-06-30 grabherr [r1] Initial check-in.
 Makefile_cxx 2011-06-30 grabherr [r1] Initial check-in.
 Makefile_deleta 2011-06-30 grabherr [r1] Initial check-in.
 Makefile_g++ 2016-11-03 grabherr [r42] Removed -ggdb3 and bounds checking.
 Makefile_g++_alpha 2011-06-30 grabherr [r1] Initial check-in.
 Makefile_g++_i386 2011-06-30 grabherr [r1] Initial check-in.
 Makefile_g++_i686 2011-06-30 grabherr [r1] Initial check-in.
 Makefile_g++_i86pc 2017-01-30 grabherr [r44] Changed Makefile.
 Makefile_g++_ia64 2011-06-30 grabherr [r1] Initial check-in.
 Makefile_g++_macosx 2011-06-30 grabherr [r1] Initial check-in.
 Makefile_g++_x86_64 2011-06-30 grabherr [r1] Initial check-in.
 Makefile_psc 2011-06-30 grabherr [r1] Initial check-in.
 Makefile_targets 2011-06-30 grabherr [r1] Initial check-in.
 README 2013-05-30 grabherr [r15] Reformatted
 test_Saguaro 2012-05-16 grabherr [r4] Added test data & script.

Read Me

Saguaro
Version 0.1, 2013/05/30

Program to detect local phylogenetic patterns in populations or species.

(c) 2011, Manfred Grabherr, Science for Life Laboratory, Department of 
Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden

Please cite: Neda Zamani, Pamela Russell, Henrik Lantz, Marc P Hoeppner, 
Jennifer RS Meadows, Nagarjun Vijay, Evan Mauceli, Federica di Palma, 
Kerstin Lindblad-Toh, Patric Jern and Manfred G Grabherr. 
Unsupervised genome-wide recognition of local relationship patterns. 
BMC Genomics 2013, 14:347



Libraries distributed with this package under LGPL:
	Spines: (c) 2010, The Broad Institute



1. Legal
--------

This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.

This library 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
Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA