ExaML 3.0.21 – Large-scale Phylogenetic Inference on Supercomputers using MPI

ExaML 3.0.21

:: DESCRIPTION

ExaML (Exascale Maximum Likelihood) implements the popular RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. It uses a radically new MPI parallelization approach that yields improved parallel efficiency, in particular on partitioned multi-gene or whole-genome datasets.

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 ExaML

:: MORE INFORMATION

Citation

ExaML Version 3: A Tool for Phylogenomic Analyses on Supercomputers.
Kozlov AM, Aberer AJ, Stamatakis A.
Bioinformatics. 2015 Mar 29. pii: btv184.

Stamatakis, A. Aberer, A.J.
Novel Parallelization Schemes for Large-Scale Likelihood-based Phylogenetic Inference
Parallel & Distributed Processing (IPDPS), 2013 IEEE 27th International Symposium Page(s):1195 – 1204

PHYLOViZ 1.0 – Phylogenetic Inference and Data Visualization for Sequence based Typing Methods

PHYLOViZ 1.0

:: DESCRIPTION

Phyloviz is platform independent JAVA software that allows the analysis of sequence-based typing methods that generate allelic profiles and their associated epidemiological data.

::DEVELOPER

PHYLOViZ team

:: SCREENSHOTS

PHYLOViZ

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java 

:: DOWNLOAD

 PHYLOViZ

:: MORE INFORMATION

Citation

PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods.
Francisco AP, Vaz C, Monteiro PT, Melo-Cristino J, Ramirez M, Carri?o JA.
BMC Bioinformatics. 2012 May 8;13:87. doi: 10.1186/1471-2105-13-87.

PHASE 2.0 – Bayesian & Maximum Likelihood Phylogenetic Inference Package

PHASE 2.0

:: DESCRIPTION

PHASE (PHylogenetics And Sequence Evolution)  is a package that performs molecular phylogenetic inference. The software seeks to accurately compare molecular sequences to determine the likely evolutionary relationships between a group of species.This package is designed specifically for use with RNA sequences that have a conserved secondary structure, e.g., rRNA and tRNA. It is well known that compensatory substitutions occur in the paired regions of RNA secondary structures; this means that substitutions occurring on one side of a pair are correlated with substitutions on the other side. Most phylogenetic programs assume that each site in a molecule evolves independently of the others but this assumption is not valid for RNA genes.

::DEVELOPER

Rattray Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

PHASE

:: MORE INFORMATION

Citation

V. Gowri-Shankar and M. Rattray.
A reversible jump method for Bayesian phylogenetic inference with a non-homogeneous substitution model” Molecular Biology and Evolution
Molecular Biology and Evolution 24(6):1286-1299 (2007).

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