The following is written for the naive user. If you know things like folders, executable files, and search path, there is no need for you to follow the instructions here. A pipeline that automatically updates reference trees using RAxML-Light when new sequences for the clade of interest appear on GenBank or are added by the user. RAxML-Light A strapped down checkpointable RAxML version for computing huge trees on supercomputers.

Raxml Github

Permalink

Join GitHub today

GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together.

Branch:master

Find file Copy path

Fetching contributors…

# Makefile August 2006 by Alexandros Stamatakis

# Makefile cleanup October 2006, Courtesy of Peter Cordes <peter@cordes.ca>

CC = clang

CFLAGS = -D_USE_PTHREADS -D__SIM_SSE3 -O2 -D_GNU_SOURCE -msse3 -fomit-frame-pointer -funroll-loops #-Wall -pedantic -Wunused-parameter -Wredundant-decls -Wreturn-type -Wswitch-default -Wunused-value -Wimplicit -Wimplicit-function-declaration -Wimplicit-int -Wimport -Wunused -Wunused-function -Wunused-label -Wno-int-to-pointer-cast -Wbad-function-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wstrict-prototypes -Wdeclaration-after-statement -Wpointer-sign -Wextra -Wredundant-decls -Wunused -Wunused-function -Wunused-parameter -Wunused-value -Wunused-variable -Wformat -Wformat-nonliteral -Wparentheses -Wsequence-point -Wuninitialized -Wundef -Wbad-function-cast

LIBRARIES = -lm -pthread

RM = rm -f

objs = axml.o optimizeModel.o multiple.o searchAlgo.o topologies.o parsePartitions.o treeIO.o models.o bipartitionList.o rapidBootstrap.o evaluatePartialGenericSpecial.o evaluateGenericSpecial.o newviewGenericSpecial.o makenewzGenericSpecial.o classify.o fastDNAparsimony.o fastSearch.o leaveDropping.o rmqs.o rogueEPA.o ancestralStates.o mem_alloc.o eigen.o

all : clean raxmlHPC-PTHREADS-SSE3

GLOBAL_DEPS = axml.h globalVariables.h rmq.h rmqs.h #mem_alloc.h compiler.h gcc.h ll_asm.h ll_list.h

raxmlHPC-PTHREADS-SSE3 : $(objs)

$(CC) -o raxmlHPC-PTHREADS-SSE3 $(objs) $(LIBRARIES) $(LDFLAGS)

#rev_functions.o : rev_functions.c $(GLOBAL_DEPS)

rmqs.o : rmqs.c $(GLOBAL_DEPS)

classify.o : classify.c $(GLOBAL_DEPS)

evaluatePartialSpecialGeneric.o : evaluatePartialSpecialGeneric.c $(GLOBAL_DEPS)

bipartitionList.o : bipartitionList.c $(GLOBAL_DEPS)

optimizeModel.o : optimizeModel.c $(GLOBAL_DEPS)

multiple.o : multiple.c $(GLOBAL_DEPS)

axml.o : axml.c $(GLOBAL_DEPS)

searchAlgo.o : searchAlgo.c $(GLOBAL_DEPS)

topologies.o : topologies.c $(GLOBAL_DEPS)

parsePartitions.o : parsePartitions.c $(GLOBAL_DEPS)

treeIO.o : treeIO.c $(GLOBAL_DEPS)

models.o : models.c $(GLOBAL_DEPS)

rapidBootstrap.o : rapidBootstrap.c $(GLOBAL_DEPS)

evaluatePartialGenericSpecial.o : evaluatePartialGenericSpecial.c $(GLOBAL_DEPS)

evaluateGenericSpecial.o : evaluateGenericSpecial.c $(GLOBAL_DEPS)

newviewGenericSpecial.o : newviewGenericSpecial.c $(GLOBAL_DEPS)

makenewzGenericSpecial.o : makenewzGenericSpecial.c $(GLOBAL_DEPS)

fastDNAparsimony.o : fastDNAparsimony.c $(GLOBAL_DEPS)

fastSearch.o : fastSearch.c $(GLOBAL_DEPS)

leaveDropping.o : leaveDropping.c $(GLOBAL_DEPS)

ancestralStates.o : ancestralStates.c $(GLOBAL_DEPS)

mem_alloc.o eigen.o : mem_alloc.c $(GLOBAL_DEPS)

eigen.o : eigen.c $(GLOBAL_DEPS)

$(CC) -c -o eigen.o eigen.c

clean :

$(RM) *.o raxmlHPC-PTHREADS-SSE3

dev : raxmlHPC-PTHREADS-SSE3

Copy lines
Copy permalink

On-line material for some old RAxML papers

Material (alignments) for 2008 Systematic Biology paper on the rapid bootstrap algorithm

test datasets available here

Material (test datasets) for 2007 Supercomputing paper on parallelizing RAxML on the IBM BlueGene/L

test datasets available here

Material for HICOMB2006 paper: 'Phylogenetic Models of Rate Heterogeneity: A High Performance Computing Perspective'

Click here for a table with the experimental raw data

Material for HPCC05 paper: “Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood”Material on RAxML-VI performance:

1,000 taxa plotalignment Alignment of 1,000 sequences from the ARB database containing Eucarya, Bacteria, Archaea by Harald Meier, TU München
1,497 taxa plot Alignment of 1,497 Bacteria by Josh Wilcox, Pace Lab, University of Colorado at Boulder, for more information on this alignment please contact the Pace Lab
1,663 taxa plotalignment Alignment of 1,663 sequences from the ARB database containing Eucarya, Bacteria, Archaea by Harald Meier, TU München
1,728 taxa plotalignment Alignment of 1,728 Archaea by Chuck Robertson, Pace Lab, University of Colorado at Boulder
2,000 taxa plotalignment Ribosomal RNA sequences by Gutell Lab, University of Texas at Austin, for more information on this alignment please contact Robin Gutell
2,560 taxa plot alignment upon requestvia email Kallersjo, M., et al., Simultaneous parsimony jackknife analysis of 2538 rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants and flowering plants. Pl. Syst. Evol., 1998. 213: p. 259-287.
4,114 taxa plotalignment 16S ribosomal Actinobacteria RNA sequences, by Usman Roshan, New Jersey Institute of Technology
6,722 taxa plotalignment Ribosomal RNA sequences by Gutell Lab, University of Texas at Austin,for more information on this alignment please contact Robin Gutell
7,769 taxa plotalignment Ribosomal RNA sequences by Gutell Lab, University of Texas at Austin, for moreinformation on this alignment please contact Robin Gutell
8,780 taxa plotalignment Alignment of 8,780 sequences from the ARB database containing Eucarya, Bacteria, Archaea. Original alignment by Harald Meier, TU München, modified by Usman Roshan, New Jersey Institute of Technology
25,057 taxa plotalignment Alignment of 25,057 Protobacteria, by Usman Roshan, New JerseyInstitute of Technology

Old Alignment Benchmark Set

Raxml Github

The old Alignment Benchmark set: includes some large real-world alignments and best-known trees for those alignments

Raxml Download For Mac