RAxML

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Contents


Authors/Maintainers

The Exelixis Lab - http://wwwkramer.in.tum.de/exelixis/software.html

Summary

RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein’s dnaml which is part of the PHYLIP package. In addition to the sequential version, RAxML offers two ways to exploit parallelism: fine-grained parallelism that can be exploited on shared memory machines or multi-core architectures and coarse-grained parallelism that can be exploited on Linux clusters. The current version of RAxML is a highly optimized program, which handles DNA and AA (amino acids) alignments under various models of substitution and several distinct methods of rate heterogeneity. In addition, it implements a significantly improved version of the fast rapid hill climbing algorithm. At the same time these new heuristics yield qualitatively comparable results. In addition to this, it also offers a novel unpublished rapid Bootstrapping algorithm that is faster by at least one order of magnitude than all other current implementations (RAxML 2.2.3, GARLI, PHYML). Once again, the results obtained by the rapid bootstrapping algorithm are qualitatively comparable to those obtained via the standard RAxML BS algorithm and, more importantly, the deviations in support values between the rapid and the standard RAxML BS algorithm are smaller than those induced by using a different search strategy, e.g., GARLI or PHYML. This rapid BS search can be combined with a rapid ML search on the original alignment and thus allows users to conduct a full ML analysis within one single program run.

RAXML comes in three flavors:

1. raxmlHPC - just the standard sequential version, compile it with gcc for LINUX and MAC.

2. raxmlHPC-PTHREADS - the Pthreads parallelized version of RAxML which is intended for shared-memory and multi-core architectures.

3. raxmlHPC-MPI the MPI-parallelized version for all types of clusters to perform parallel bootstraps, rapid parallel bootstraps, or multiple inferences on the original alignment.

Other compilers: The Intel-compiler icc can produce produces 20-30% faster code than gcc.


Features

  • Listed features

Architectural/Functional Overview

  • high level design info, how it works, performance - may be a link, or several links

Usage Overview

  • If possible with small example - may be a link

Dependacies

gcc, mpicc

HP-SEE Applications

DNAMA (DNA multicore analysis)

Resource Centers

RAXML is installed at Bulgarian HPC under user account.

Usage by Other Projects and Communities

  • If any

Recommendations for Configuration and Usage

Please describe here any common settings, configurations or conventions that would make the usage of this resource (library or tool) more interoperable or scalable across the HP-SEE resources. These recommendations should include anything that is related to the resource and is agreed upon by administrators and users, or across sites and applications. These recommendations should emerge from questions or discussions opened by site administrators or application developers, at any stage, including installation, development, usage, or adaptation for another HPC centre.

Provided descriptions should describe general or site specific aspects of resource installation, configuration and usage, or describe the guidelines or convention for deploying or using the resource within the local (user/site) or temporary environment (job). Examples are:

  • Common configuration settings of execution environment
  • Filesystem path or local access string
  • Environment variables to be set or used by applications
  • Options (e.g. additional modules) that are needed or required by applications and should be present
  • Minimum quantitative values (e.g. quotas) offered by the site
  • Location and format of some configuration or usage hint instructing applications on proper use of the resource or site specific policy
  • Key installation or configuration settings that should be set to a common value, or locally tweaked by local site admins
  • Conventions for application or job bound installation and usage of the resource
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