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Latest commit d0b7206 Jul 20, 2016 @stamatak updated manual
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WindowsExecutables_v8.2.4 added version 8.2.4 windows executables Dec 9, 2015
WindowsExecutables_v8.2.7_Alternate added new windows executables by ingo michalak Mar 17, 2016
manual updated manual Jul 20, 2016
usefulScripts use more portabel perl shebangs Dec 7, 2014
.gitignore Restrict .gitignore to main folder only Mar 2, 2016
Makefile.AVX.HYBRID.gcc added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
Makefile.AVX.MPI.gcc added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
Makefile.AVX.PTHREADS.gcc added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
Makefile.AVX.PTHREADS.mac added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
Makefile.AVX.gcc removed old 3rd part windows executables Mar 17, 2016
Makefile.AVX.mac added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
Makefile.AVX2.HYBRID.gcc added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
Makefile.AVX2.MPI.gcc added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
Makefile.AVX2.PTHREADS.gcc added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
Makefile.AVX2.PTHREADS.mac added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
Makefile.AVX2.gcc added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
Makefile.AVX2.mac added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
Makefile.HYBRID.gcc added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
Makefile.MPI.gcc added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
Makefile.PTHREADS.gcc added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
Makefile.PTHREADS.mac added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
Makefile.QuartetMPI.gcc added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
Makefile.SSE3.HYBRID.gcc added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
Makefile.SSE3.MPI.gcc added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
Makefile.SSE3.PTHREADS.gcc added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
Makefile.SSE3.PTHREADS.mac added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
Makefile.SSE3.QuartetMPI.gcc added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
Makefile.SSE3.gcc added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
Makefile.SSE3.mac added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
Makefile.gcc added modified makefiles that will do a clean build (i.e. remove all … Aug 10, 2015
README update readme Jul 20, 2016
ancestralStates.c -added ancestral state computation for LG4X and LG4M models Apr 10, 2015
avxLikelihood.c 1. updated the manual Jul 30, 2014
axml.c added flag: --print-identical-sequences that will tell RAxML to remov… Jul 20, 2016
axml.h added flag: --print-identical-sequences that will tell RAxML to remov… Jul 20, 2016
bipartitionList.c -added more verbose tree parser error messages for multi-furcating tr… Mar 10, 2016
classify.c fixed major bug in likelihood functions for partitioned analyses with… Jun 25, 2015
eigen.c cleaned up the code Aug 5, 2015
evaluateGenericSpecial.c fixed two bugs: Oct 2, 2015
evaluatePartialGenericSpecial.c added some experimental stuff for bastien to play with Nov 21, 2014
fastDNAparsimony.c some native windows-compilation related fixes Mar 10, 2016
fastSearch.c added some experimental stuff for bastien to play with Nov 21, 2014
globalVariables.h added new protein subst model stmtREV, see: http://datadryad.org/reso… Dec 27, 2014
gpl-3.0.txt added GPL license Nov 17, 2014
leaveDropping.c -added an automatic option to compute the SH-like support values (-f … Jul 16, 2013
legacyCode.c some code cleanup Jul 31, 2014
makenewzGenericSpecial.c fixed two bugs: Oct 2, 2015
mem_alloc.c added better error reporting for cases where RAxML runs out of memory Feb 19, 2014
models.c added Kassian's code for TC/IC score calculations on partial gene trees Jul 9, 2015
multiple.c -added more verbose tree parser error messages for multi-furcating tr… Mar 10, 2016
newviewGenericSpecial.c fixed two bugs: Oct 2, 2015
optimizeModel.c 1. changed BS replicate generation option -f j to refuse generating B… Feb 26, 2016
parsePartitions.c added an assertion Aug 5, 2015
rapidBootstrap.c added some experimental stuff for bastien to play with Nov 21, 2014
rmq.h changed source file permissions Jan 16, 2014
rmqs.c fixed minor type casting issues and minor bug in error detection outp… Apr 13, 2014
rmqs.h changed source file permissions Jan 16, 2014
rogueEPA.c -fixed some minor compiler issues with the Makefiles and source files Jun 24, 2013
searchAlgo.c added some experimental stuff for bastien to play with Nov 21, 2014
topologies.c Added ultra-fast RELL bootstrapping that can be invoked via -f D as d… Nov 15, 2013
treeIO.c made tree parsing error reporting even more verbose Mar 10, 2016

README

Standard RAxML version 8.2.9

============================================================================================================

When using RAxML please cite the following paper:

A. Stamatakis: "RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies". 
Bioinformatics (2014) 30 (9): 1312-1313.

============================================================================================================

Quick start under Linux:

standard, SSE3 or AVX version?

In general you should try to compile the SSE3 version that makes use of capabilities 
on relativiely recent processors (most Intel or AMD chips not older than 3-4 years).
The SSE3 version will run about 40% faster than the non-SSE3 version.

If you have a more recently bought processor (within the last 1-2 years), please also try to compile
the AVX version which once again uses the capabilities of modern processors better and can be 10-30% faster 
than the SSE3 version. AVX will work on the Intel i7 (sandy-bridge) series processors as well as on the very recently 
released AMD Bulldozer systems. 

Compiling should work out of the box with all reasonably recent vesrion of the GNU gcc and Intel icc compilers.
If you want to use icc replace gcc by icc in the Makefiles.

Please direct all your RAxML questions to our google group (and only after 
having used the search function!): 
https://groups.google.com/forum/?hl=de&fromgroups#!forum/raxml

Sequential version:

type:
"make -f Makefile.gcc"
"rm *.o"
or
"make -f Makefile.SSE3.gcc"
"rm *.o"
or
"make -f Makefile.AVX.gcc"
"rm *.o"

Pthreads version:

type: 
"make -f Makefile.PTHREADS.gcc"
"rm *.o"
or
"make -f Makefile.SSE3.PTHREADS.gcc"
"rm *.o"
or
"make -f Makefile.AVX.PTHREADS.gcc"
"rm *.o"

Coarse-grain MPI version:

type:
"make -f Makefile.MPI.gcc"
"rm *.o"
or
"make -f Makefile.SSE3.MPI.gcc"
"rm *.o"
or
"make -f Makefile.AVX.MPI.gcc"                            
"rm *.o"

Hybrid MPI/Pthreads version:

Before using this version, please read this paper here:

http://sco.h-its.org/exelixis/pubs/Exelixis-RRDR-2010-3.pdf

and look at these slides: 

http://sco.h-its.org/exelixis/resource/doc/Phylo100225.pdf

type:
"make -f Makefile.HYBRID.gcc" 
"rm *.o"
or  
"make -f Makefile.SSE3.HYBRID.gcc"
"rm *.o"
or
"make -f Makefile.AVX.HYBRID.gcc" 
"rm *.o"