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Octocat-spinner-32 WindowsExecutables_v8.0.17 updated windows executables March 25, 2014
Octocat-spinner-32 manual updated manual April 18, 2014
Octocat-spinner-32 usefulScripts fixed bug in script: applyRAxML2AllFilesInDirectory.pl January 30, 2014
Octocat-spinner-32 Makefile.AVX.HYBRID.gcc fixed some typos in the printouts, made the makefiles debian compliant March 19, 2014
Octocat-spinner-32 Makefile.AVX.MPI.gcc fixed some typos in the printouts, made the makefiles debian compliant March 19, 2014
Octocat-spinner-32 Makefile.AVX.PTHREADS.gcc fixed some typos in the printouts, made the makefiles debian compliant March 19, 2014
Octocat-spinner-32 Makefile.AVX.PTHREADS.mac Fixed Makefiles for Macintosh using clang compiler. March 25, 2014
Octocat-spinner-32 Makefile.AVX.gcc fixed some typos in the printouts, made the makefiles debian compliant March 19, 2014
Octocat-spinner-32 Makefile.AVX.mac Fixed Makefiles for Macintosh using clang compiler. March 25, 2014
Octocat-spinner-32 Makefile.AVX2.HYBRID.gcc fixed some typos in the printouts, made the makefiles debian compliant March 19, 2014
Octocat-spinner-32 Makefile.AVX2.MPI.gcc fixed some typos in the printouts, made the makefiles debian compliant March 19, 2014
Octocat-spinner-32 Makefile.AVX2.PTHREADS.gcc fixed some typos in the printouts, made the makefiles debian compliant March 19, 2014
Octocat-spinner-32 Makefile.AVX2.PTHREADS.mac Fixed Makefiles for Macintosh using clang compiler. March 25, 2014
Octocat-spinner-32 Makefile.AVX2.gcc fixed some typos in the printouts, made the makefiles debian compliant March 19, 2014
Octocat-spinner-32 Makefile.AVX2.mac Fixed Makefiles for Macintosh using clang compiler. March 25, 2014
Octocat-spinner-32 Makefile.HYBRID.gcc fixed some typos in the printouts, made the makefiles debian compliant March 19, 2014
Octocat-spinner-32 Makefile.MPI.gcc fixed some typos in the printouts, made the makefiles debian compliant March 19, 2014
Octocat-spinner-32 Makefile.PTHREADS.gcc fixed some typos in the printouts, made the makefiles debian compliant March 19, 2014
Octocat-spinner-32 Makefile.PTHREADS.mac Fixed Makefiles for Macintosh using clang compiler. March 25, 2014
Octocat-spinner-32 Makefile.QuartetMPI.gcc fixed some typos in the printouts, made the makefiles debian compliant March 19, 2014
Octocat-spinner-32 Makefile.SSE3.HYBRID.gcc fixed some typos in the printouts, made the makefiles debian compliant March 19, 2014
Octocat-spinner-32 Makefile.SSE3.MPI.gcc fixed some typos in the printouts, made the makefiles debian compliant March 19, 2014
Octocat-spinner-32 Makefile.SSE3.PTHREADS.gcc fixed some typos in the printouts, made the makefiles debian compliant March 19, 2014
Octocat-spinner-32 Makefile.SSE3.PTHREADS.mac Fixed Makefiles for Macintosh using clang compiler. March 25, 2014
Octocat-spinner-32 Makefile.SSE3.QuartetMPI.gcc fixed some typos in the printouts, made the makefiles debian compliant March 19, 2014
Octocat-spinner-32 Makefile.SSE3.gcc fixed some typos in the printouts, made the makefiles debian compliant March 19, 2014
Octocat-spinner-32 Makefile.SSE3.mac Fixed Makefiles for Macintosh using clang compiler. March 25, 2014
Octocat-spinner-32 Makefile.gcc fixed some typos in the printouts, made the makefiles debian compliant March 19, 2014
Octocat-spinner-32 README fixed minor type casting issues and minor bug in error detection outp… April 13, 2014
Octocat-spinner-32 Release-Notes fixed minor type casting issues and minor bug in error detection outp… April 13, 2014
Octocat-spinner-32 ancestralStates.c -fixed some minor compiler issues with the Makefiles and source files June 24, 2013
Octocat-spinner-32 avxLikelihood.c Added substitution models that use the ascertainment bias, also know … October 29, 2013
Octocat-spinner-32 axml.c fixed minor type casting issues and minor bug in error detection outp… April 13, 2014
Octocat-spinner-32 axml.h fixed minor type casting issues and minor bug in error detection outp… April 13, 2014
Octocat-spinner-32 bipartitionList.c fixed minor type casting issues and minor bug in error detection outp… April 13, 2014
Octocat-spinner-32 classify.c -fixed a bug in the error checking function March 27, 2014
Octocat-spinner-32 eigen.c -put eigenvalue/eigenvector decomposition into separate file that is … December 13, 2013
Octocat-spinner-32 evaluateGenericSpecial.c Fixed an issue with an assertion for the likelihood calculations that… February 28, 2014
Octocat-spinner-32 evaluatePartialGenericSpecial.c -fixed some minor compiler issues with the Makefiles and source files June 24, 2013
Octocat-spinner-32 fastDNAparsimony.c general cleanup of random number generators November 13, 2013
Octocat-spinner-32 fastSearch.c Fixed bugs in: March 25, 2014
Octocat-spinner-32 globalVariables.h MPI and hybrid MPI/Pthreads versions now also support RELL bootstraps. November 16, 2013
Octocat-spinner-32 leaveDropping.c -added an automatic option to compute the SH-like support values (-f … July 16, 2013
Octocat-spinner-32 makenewzGenericSpecial.c 1. fixed a bug in the LG4X protein substitution model March 28, 2014
Octocat-spinner-32 mem_alloc.c added better error reporting for cases where RAxML runs out of memory February 19, 2014
Octocat-spinner-32 models.c 1. fixed a bug in the LG4X protein substitution model March 28, 2014
Octocat-spinner-32 multiple.c updated manual March 21, 2014
Octocat-spinner-32 newviewGenericSpecial.c 1. fixed a bug in the LG4X protein substitution model March 28, 2014
Octocat-spinner-32 optimizeModel.c 1. fixed a bug in the LG4X protein substitution model March 28, 2014
Octocat-spinner-32 parsePartitions.c fixed some typos in the printouts, made the makefiles debian compliant March 19, 2014
Octocat-spinner-32 rapidBootstrap.c updated manual March 21, 2014
Octocat-spinner-32 rmq.h changed source file permissions January 16, 2014
Octocat-spinner-32 rmqs.c fixed minor type casting issues and minor bug in error detection outp… April 13, 2014
Octocat-spinner-32 rmqs.h changed source file permissions January 16, 2014
Octocat-spinner-32 rogueEPA.c -fixed some minor compiler issues with the Makefiles and source files June 24, 2013
Octocat-spinner-32 searchAlgo.c -added -H option that allows to disable pattern compression December 09, 2013
Octocat-spinner-32 topologies.c Added ultra-fast RELL bootstrapping that can be invoked via -f D as d… November 15, 2013
Octocat-spinner-32 treeIO.c updated manual March 21, 2014
README
Standard RAxML version 8.0.20

Compiling 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/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"
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