STS 0.1 – Phylogenetic Inference program via Sequential Monte Carlo

STS 0.1

:: DESCRIPTION

STS (Sequential Tree Sampler) is a software for phylogenetic inference program via sequential Monte Carlo.

::DEVELOPER

The Darling Lab , Erick Matsen’s group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 STS

:: MORE INFORMATION

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

ERATE 0.8 – Maximum Likelihood Phylogenetic Inference

ERATE 0.8

:: DESCRIPTION

erate is an extension of Joe Felsenstein’s DNAML program which treats insertions and deletions as evolutionary events, rather than ignoring them as missing data (which is what the most widely used phylogenetic inference programs all do).

::DEVELOPER

Elena Rivas, Eddy lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ERATE

:: MORE INFORMATION

Citation

Probabilistic Phylogenetic Inference with Insertions and Deletions.
E. Rivas, S. R. Eddy.
PLoS Comput. Biol., 4:e1000172, 2008.

PIPS 1.0 – Phylogenetic Inference of Protein Stability

PIPS 1.0

:: DESCRIPTION

PIPS (Phylogenetic Inference of Protein Stability) was used to analyze cold shock protein, ribonuclease HI, thioredoxin, and H1 influenza hemagglutinin

::DEVELOPER

Bloom Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PIPS

:: MORE INFORMATION

Citation

Jesse D. Bloom and Matthew J. Glassman.
Inferring stabilizing mutations from protein phylogenies: application to influenza hemagglutinin.”
PLoS Comput. Biol. 5:e1000349 (2009)

ProtEvol 1.0 – Maximum Likelihood Phylogenetic Inference with Selection on Protein Folding Stability

ProtEvol 1.0

:: DESCRIPTION

The program ProtEvol performs two kinds of computation.

  1. It computes the mean-field site-specific amino acid distributions that have minimal differences with respect to the background distribution and that constraint the average stability of the native state of the protein against both unfolding and misfolding. The program also computes an exchangeability matrix derived from an empirical substitution model or from a mutation model that can be used together with the site-specific distributions for applications in phylogenetic inference.
  2. It simulates protein evolution subject to the constraint of selection on the folding stability of the native state of the protein against both unfolding and misfolding.

::DEVELOPER

Unidad de Bioinformatica CBMSO

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  ProtEvol

:: MORE INFORMATION

Citation

Maximum likelihood phylogenetic inference with selection on protein folding stability.
Arenas M, Sánchez-Cobos A, Bastolla U.
Mol Biol Evol. 2015 Apr 2. pii: msv085.

REPHINE 0.9 – REcursive PHylogenetic INferencE

REPHINE 0.9

:: DESCRIPTION

REPHINE implements a recursive tree-fitting and search procedure which aims to address the problem of fitting phylogenies to sequence datasets that include both closely and distantly related species.

::DEVELOPER

Joe Miller

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 REPHINE

:: MORE INFORMATION

SlidingBayes 0.94 – Exploring Recombination using a Sliding window approach based on Bayesian Phylogenetic inference

SlidingBayes 0.94

:: DESCRIPTION

SlidingBayes is a tool for Bayesian scanning analysis to detect recombination or discordant phylogenetic relationships throughout a nucleotide or amino acid alignment. Bayesian scanning resembles the bootscanning analysis in the way that Bayesian inference analysis is performed in a sliding window of a specified length, and the support of every single clade (approximate posterior probabilities instead of the bootstrap values) is plotted throughout the alignment.

::DEVELOPER

Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research

:: SCREENSHOTS

SlidingBayes

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • Java

:: DOWNLOAD

 SlidingBayes

:: MORE INFORMATION

Citation

Bioinformatics. 2005 Apr 1;21(7):1274-5. Epub 2004 Nov 16.
SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference.
Paraskevis D1, Deforche K, Lemey P, Magiorkinis G, Hatzakis A, Vandamme AM.

Bayes – Modeling Incomplete Alignments in Phylogenetic Inference

Bayes

:: DESCRIPTION

Bayes is a statistical method for inferring phylogenetic trees from EST-based incomplete MSA data.

::DEVELOPER

Mayetri Gupta

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package

:: DOWNLOAD

 Bayes

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Mar 1;25(5):592-8. doi: 10.1093/bioinformatics/btp015.
A hierarchical model for incomplete alignments in phylogenetic inference.
Cheng F, Hartmann S, Gupta M, Ibrahim JG, Vision TJ.

Phylo-SMC r0 – Bayesian Phylogenetic Inference tool based on Sequential Monte Carlo

Phylo-SMC r0

:: DESCRIPTION

Phylo-SMC is a Bayesian phylogenetic inference tool based on Sequential Monte Carlo (SMC), an alternative to the standard Markov Chain Monte Carlo approach (MCMC).

::DEVELOPER

Alexandre BouchardSriram Sankararaman, and Michael I. Jordan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX / Windows
  • Java
  • Phylip
  • Mrbayes
  • R package

:: DOWNLOAD

 Phylo-SMC

:: MORE INFORMATION

Citation

Syst Biol. 2012 Jul;61(4):579-93. doi: 10.1093/sysbio/syr131.
Phylogenetic inference via sequential Monte Carlo.
Bouchard, A., Sankararaman, S., Jordan, M.I

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.