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RAxML Version 8: A Tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies

January 2014
Bioinformatics 30(9)

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Heidelberger Institut für Theoretische Studien

Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. I present some of the most notable new features and extensions of RAxML, such as, a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX, and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date, 50 page user manual covering all new RAxML options is available. The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Alexandros.Stamatakis@h-its.org.

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Vol. 30 no. 9 2014, pages 1312–1313

BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/btu033

Phylogenetics Advance Access publication January 21, 2014

RAxML version 8: a tool for phylogenetic analysis and

post-analysis of large phylogenies

Alexandros Stamatakis

1,2

Scientific Computing Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg and

Department of

Informatics, Institute of Theoretical Informatics, Karlsruhe Institute of Technology, 76128 Karlsruhe, Germany

Associate Editor: Jonathan Wren

ABSTRACT

Motivation: Phylogenies are increasingly used in all fields of medical

and biological research. Moreover, because of the next-generation

sequencing revolution, datasets used for conducting phylogenetic

analyses grow at an unprecedented pace. RAxML (Randomized

Axelerated Maximum Likelihood) is a popular program for phylogen-

etic analyses of large datasets under maximum likelihood. Since the

last RAxML paper in 2006, it has been continuously maintained and

extended to accommodate the increasingly growing input datasets

and to serve the needs of the user community.

Results: I present some of the most notable new features and

extensions of RAxML, such as a substantial extension of substitution

models and supported data types, the introduction of SSE3, AVX and

AVX2 vector intrinsics, techniques for reducing the memory require-

ments of the code and a plethora of operations for conducting post-

analyses on sets of trees. In addition, an up-to-date 50-page user

manual covering all new RAxML options is available.

Availability and implementation: The code is available under GNU

GPL at https://github.com/stamatak/standard-RAxML.

Contact: alexandros.stamatakis@h-its.org

Supplementary information: Supplementary data are available at

Bioinformatics online.

Received on December 22, 2013; revised and accepted on

January 14, 2014

1INTRODUCTION

RAxML (Randomized Axelerated Maximum Likelihood) is a

popular program for phylogenetic analysis of large datasets

under maximum likelihood. Its major strength is a fast maximum

likelihood tree search algorithm that returns trees with good

likelihood scores. Since the last RAxML paper (Stamatakis,

2006), it has been continuously maintained and extended to ac-

commodate the increasingly growing input datasets and to serve

the needs of the user community. In the following, I will present

some of the most notable new features and extensions of RAxML.

2 NEW FEATURES

2.1 Bootstrapping and support values

RAxML offers four different ways to obtain bootstrap support.

It implements the standard non-parametric bootstrap and also

the so-called rapid bootstrap (Stamatakis et al., 2008), which is a

standard bootstrap search that relies on algorithmic shortcuts

and approximations to speed up the search process.

It also offers an option to calculate the so-called SH-like

support values (Guindon et al., 2010). I recently implemented

a method that allows for computing RELL (Resampling

Estimated Log Likelihoods) bootstrap support as described by

Minh et al. (2013).

Apart from this, RAxML also offers a so-called bootstopping

option (Pattengale et al.,2010).Whenthisoptionisused,

RAxML will automatically determine how many bootstrap rep-

licates are required to obtain stable support values.

2.2 Models and data types

Apart from DNA and protein data, RAxML now also supports

binary, multi-state morphological and RNA secondary structure

data. It can correct for ascertainment bias (Lewis, 2001) for all of

the above data types. This might be useful not only for morpho-

logical data matrices that only contain variable sites but also for

alignments of SNPs.

The number of available protein substitution models has been

significantly extended and comprises a general time reversible

(GTR) model, as well as the computationally more complex

LG4M and LG4X models (Le et al., 2012). RAxML can also

automatically determine the best-scoring protein substitution

model.

Finally, a new option for conducting a maximum likelihood

estimate of the base frequencies has become available.

2.3 Parallel versions

RAxML offers a fine-grain parallelization of the likelihood func-

tion for multi-core systems via the PThreads-based version and a

coarse-grain parallelization of independent tree searches via MPI

(Message Passing Interface). It also supports coarse-grain/fine-

grain parallelism via the hybrid MPI/PThreads version (Pfeiffer

and Stamatakis, 2010).

Note that, for extremely large analyses on supercomputer s,

using the dedicated sister program ExaML [Exascale Maximum

Likelihood (Stamatakis and Aberer, 2013)] is recommended.

2.4 Post-analysis of trees

RAxML offers a plethora of post-analysis functions for sets of

trees. Apart from standard statistical significance tests, it offers

efficient (and partially parallelized) operations for computing

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Robinson–Foulds distances, as well as extended majority rule,

majority rule and strict consensus trees (Aberer et al., 2010).

Beyond this, it implements a method for identifying the so-

called rogue taxa (Pattengale et al., 2011), and I recently imple-

mented options for calculating the TC (Tree Certainty) and IC

(Internode Certainty) measures as introduced by Salichos and

Rokas (2013).

Finally, there is the new plausibility checker option (Dao et al.,

2013) that allows computing the RF distances between a huge phyl-

ogeny with tens of thousands of taxa and several smaller more

accurate reference phylogenies that contain a strict subset of the

taxa in the huge tree. This option can be used to automatically

assess the quality of huge trees that can not be inspected by eye.

2.5 Analyzing next-generation sequencing data

RAxML offers two algorithms for preparing and analyzing next-

generation sequencing data. A sliding-window approach (unpub-

lished) is available to assess which regions of a gene (e.g. 16S)

exhibit strong and stable phylogenetic signal to support decisions

about which regions to amplify. Apart from that, RAxML also

implements parsimony and maximum likelihood flavors of the

evolutionary placement algorithm [EPA (Berger et al., 2011)]

that places short reads into a given reference phylogeny obtained

from full-length sequences to determine the evolutionary origin

of the reads. It also offers placement support statistics for those

reads by calculating likelihood weights. This option can also be

used to place fossils into a given phylogeny (Berger and

Stamatakis, 2010) or to insert different outgroups into the tree

a posteriori, that is, after the inference of the ingroup phylogeny.

2.6 Vector intrinsics

RAxML uses manually inserted and optimized x86 vector intrin-

sics to accelerate the parsimony and likelihood calculations.

It supports SSE3, AVX and AVX2 (using fused multiply-add

instructions) intrinsics. For a small single-gene DNA alignment

using the  model of rate heterogeneity, the unvectorized version

of RAxML requires 111.5 s, the SSE3 version 84.4 s and the

AVX version 66.22 s to complete a simple tree search on an

Intel i7-2620 M core running at 2.70 GHz under Ubuntu Linux.

The differences between AVX and AVX2 are less pronounced

and are typically below 5% run time improvement.

2.7 Saving memory

Because memory shortage is becoming an issue due to the grow-

ing dataset sizes, RAxML implements an option for reducing

memory footprints and potentially run times on large phyloge-

nomic datasets with missing data. The memory savings are pro-

portional to the amount of missing data in the alignment

(Izquierdo-Carrasco et al.,2011)

2.8 Miscellaneous new options

RAxML offers options to conduct fast and more superficial tree

searches on datasets with tens of thousands of taxa. It can also

compute marginal ancestral states and offers an algorithm for

rooting trees. Furthermore, it implements a sequential,

PThreads-parallelized and MPI-parallelized algorithm for com-

puting all quartets or a subset of quartets for a given alignment.

3 USER SUPPORT AND FUTURE WORK

User support is provided via the RAxML Google group

at: https://groups.google.com/forum/?hl¼en#!forum/raxml. The

RAxML source code contains a comprehensive manual and

there is a step-by-step tutorial with some basic commands avail-

able at http://www.exelixis-lab.org/web/software/raxml/hands_

on.html. Further resources are available via the RAxML soft-

ware page at http://www.exelixis-lab.org/web/software/raxml/

Future work includes the continued maintenance of RAxML,

the adaptation to novel computer architectures and the implemen-

tation of novel models and datatypes, in particular codon models.

ACKNOWLEDGEMENT

The author thank several colleagues for contributing code to

RAxML: Andre J. Aberer, Simon Berger, Alexey Kozlov, Nick

Pattengale, Wayne Pfeiffer, Akifumi S. Tanabe, David Dao and

Charlie Taylor.

Funding: This work was funded by institutional funding provided

by the Heidelberg Institute for Theoretical Studies.

Conflict of Interest: none declared.

REFERENCES

Aberer,A.J. et al. (2010) Parallelized phylogenetic post-analysis on multi-core archi-

tectures. J. Comput. Sci., 1, 107–114.

Berger,S.A. and Stamatakis,A. (2010) Accuracy of morphology-based phylogenetic

fossil placement under maximum likelihood. In: International Conference on

Computer Systems and Applications (AICCSA), 2010 IEEE/ACS.IEEE,

New York, USA, pp. 1–9.

Berger,S.A. et al. (2011) Performance, accuracy, and web server for evolutionary

placement of short sequence reads under maximum likelihood. Syst. Biol., 60,

291–302.

Dao,D. et al. (2013) Automated plausibility analysis of large phyolgenies. Technical

report. Karlsruhe Institute of Technology.

Guindon,S. et al. (2010) New algorithms and methods to estimate maximum-like-

lihood phylogenies: assessing the performance of phyml 3.0. Syst. Biol., 59,

307–321.

Izquierdo-Carrasco,F. et al. (2011) Algorithms, data structures, and numerics

for likelihood-based phylogenetic inference of huge trees. BMC

Bioinformatics, 12,470.

Le,S.Q. et al. (2012) Modeling protein evolution with several amino acid replace-

ment matrices depending on site rates. Mol. Biol. Evol., 29, 2921–2936.

Lewis,P.O. (2001) A likelihood approach to estimating phylogeny from discrete

morphological character data. Syst. Biol., 50, 913–925.

Minh,B.Q. et al. (2013) Ultrafast approximation for phylogenetic bootstrap. Mol.

Biol Evol., 30, 1188–1195.

Pattengale,N.D. et al. (2010) How many bootstrap replicates are necessary?

J. Comput. Biol., 17, 337–354.

Pattengale,N.D. et al. (2011) Uncovering hidden phylogenetic consensus in large

data sets. IEEE/ACM Trans. Comput. Biol. Bioinforma., 8, 902–911.

Pfeiffer,W. and Stamatakis,A. (2010) Hybrid mpi/pthreads parallelization of the

raxml phylogenetics code. In International Symposium on Parallel &

Distributed Processing, Workshops and Phd Forum (IPDPSW), 2010 IEEE.

IEEE, New York, USA, pp. 1–8.

Salichos,L. and Rokas,A. (2013) Inferring ancient divergences requires genes with

strong phylogenetic signals. Nature, 497, 327–331.

Stamatakis,A. (2006) Raxml-vi-hpc: maximum likelihood-based phylogenetic ana-

lyses with thousands of taxa and mixed models. Bioinformatics, 22

, 2688–2690.

Stamatakis,A. and Aberer,A. (2013) Novel parallelization schemes for large-scale

likelihood-based phylogenetic inference. In IEEE 27th International Symposium

on Parallel Distributed Processing (IPDPS), 2013. pp. 1195–1204.

Stamatakis,A. et al. (2008) A rapid bootstrap algorithm for the raxml web servers.

Syst. Biol., 57, 758–771.

1313

RAxML version 8

Supplementary Data

Data

January 2014

Alexandros Stamatakis

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Full-text available

May 2010

Abstract-A hybrid MPI/Pthreads parallelization was implemented in the RAxML phylogenetics code. New MPI code was added to the existing Pthreads production code to exploit parallelism at two algorithmic levels simultaneously: coarse-grained with MPI and fine-grained with Pthreads. This hybrid, multi-grained approach is well suited for current high-performance computers, which typically are clusters of multicore, shared-memory nodes. The hybrid version of RAxML is especially useful for a comprehensive phylogenetic analysis, i.e., execution of many rapid bootstraps followed by a full maximum likelihood search. Multiple multi-core nodes can be used in a single run to speed up the computation and, hence, reduce the turnaround time. The hybrid code also allows more efficient utilization of a given number of processor cores. Moreover, it often returns a better solution than the stand-alone Pthreads code, because additional maximum likelihood searches are conducted in parallel using MPI. The comprehensive analysis algorithm involves four stages, in which coarse-grained parallelism continually decreases from stage to stage. The first three stages speed up well with MPI, while the last stage speeds up only with Pthreads. This leads to a tradeoff in effectiveness between MPI and Pthreads parallelization. The useful number of MPI processes increases with the number of bootstraps performed, but typically is limited to 10 or 20 by the parameters of the algorithm. The optimal number of Pthreads increases with the number of distinct patterns in the columns of the multiple sequence alignment, but is limited to the number of cores per node of the computer being used. For a benchmark problem with 218 taxa, 1,846 patterns, and 100 bootstraps run on the Dash computer at SDSC, the speedup of the hybrid code on 10 nodes (80 cores) was 6.5 compared to the Pthreads-only code on one node (8 cores) and 35 compared to the serial code. This run used 10 MPI processes with 8 Pthreads each. For an- - other problem with 125 taxa, 19,436 patterns, and 100 bootstraps, the speedup on the Triton PDAF computer at SDSC was 38 on two nodes (64 cores) compared to the serial code. This run used 2 MPI processes with 32 Pthreads each.

A rapid Bootstrap algorithm for the RAxML Web Servers

Article

Jan 2008

Novel Parallelization Schemes for Large-Scale Likelihood-based Phylogenetic Inference

Conference Paper

May 2013

The molecular data avalanche generated by novel wet-lab sequencing technologies allows for reconstructing phylogenies (evolutionary trees) using hundreds of complete genomes as input data. Therefore, scalable codes are required to infer trees on these data under likelihood-based models of molecular evolution. We recently introduced a checkpointable and scalable MPI-based code for this purpose called RAxML-Light and are currently using it for several real-world data analysis projects. It turned out that the scalability of RAxML-Light is nonetheless still limited because of the fork-join parallelization approach that is deployed. To this end, we introduce a novel, generally applicable, approach to computing the phylogenetic likelihood in parallel on whole-genome datasets and implement it in ExaML (Exascale Maximum Likelihood). ExaML executes up to 3.2 times faster than RAxML-Light because of the more efficient parallelization and communication scheme, while implementing exactly the same tree search algorithm. Moreover, the new parallelization approach exhibits lower code complexity and a more appropriate structure for implementing fault tolerance with respect to hardware failures.

2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops & PhD Forum [ASHES Introduction]

Conference Paper

Jan 2012

Parasuraman Balaji

This workshop focuses on understanding the implications of accelerators on the architectures and programming environments of future systems. It seeks to ground accelerator research through studies of application kernels or whole applications on such systems, as well as tools and libraries that improve the performance or productivity of applications trying to use these systems. The goal of this workshop is to bring together researchers and practitioners who are involved in application studies for accelerators and other hybrid systems, to learn the opportunities and challenges in future design trends for HPC applications and systems.

Automated Plausibility Analysis of Large Phylogenies

Article

Jan 2013

This chapter introduces a new approach to assess the plausibility of large phylogenies by computing all pairwise topological Robinson-Foulds (RF) distances of a 55, taxon tree of plants, for instance, and a set containing a large number of substantially smaller reference trees. It first presents a naive and then an effective algorithm for inducing subtrees. The chapter then provides an experimental evaluation of both algorithms using simulated and real data from STBase. The chapter describes a novel method for speeding up the computation of induced subtrees from a given leaf set. The key idea is to root the large tree at an inner node and compute the lowest common ancestor (LCA) of each and every pair of leaves in the leaf set. Finally, the chapter presents a straightforward implementation of the plausibility-check algorithm. The authors have implemented the algorithm in C as part of RAxML.