Tag: Phylogenetic Inference

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.

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 Bouchard, Sriram 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

phylostan – Phylogenetic Inference using Stan

phylostan

 

:: DESCRIPTION

phylostan is a tool written in python for inferring phylogenetic trees from nucleotide datasets. It generates a variety of phylogenetic models using the Stan language.

::DEVELOPER

Mathieu Fourment

 SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

phylostan

:: MORE INFORMATION

JolyTree 2.1 – Fast Distance-based Phylogenetic Inference from unaligned Genome Sequences

JolyTree 2.1

:: DESCRIPTION

JolyTree implements an alignment-free distance-based procedure for inferring phylogenetic trees from genome contig sequences. For each pair of genomes, a dissimilarity measure is first computed and next transformed to obtain an estimation of the number of substitution events that have occurred during their evolution.

::DEVELOPER

Alexis Criscuolo (alexis.criscuolo@pasteur.fr)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/  MacOsX

:: DOWNLOAD

JolyTree

:: MORE INFORMATION

Citation

Alexis Criscuolo,
A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies
Research Ideas and Outcomes, 2019, 5:e36178.

ALFRED-G – Distance Estimator for Phylogenetic Inference

ALFRED-G

:: DESCRIPTION

ALFRED-G is an Alignment Free Distance Estimator software for Phylogenetic Inference. It takes as input a set of n sequences and ouputs an n x n matrix of distance estimate for use in Phylogenetic inference.

::DEVELOPER

Prof. Srinivas Aluru Research group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ALFRED-G

:: MORE INFORMATION

Citation

Thankachan SV, Chockalingam SP, Liu Y, Krishnan A, Aluru S.
A greedy alignment-free distance estimator for phylogenetic inference.
BMC Bioinformatics. 2017 Jun 7;18(Suppl 8):238. doi: 10.1186/s12859-017-1658-0. PMID: 28617225; PMCID: PMC5471951.

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.

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.

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)

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.