HyPhy 2.5.31 – Hypothesis testing using Phylogenies

HyPhy 2.5.31

:: DESCRIPTION

HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environmen. HyPhy intended to perform maximum likelihood analyses of genetic sequence data and equipped with tools to test various statistical hypotheses. HYPHY was designed with maximum flexibility in mind and to that end it incorporates a simple high level programming language which enables the user to tailor the analyses precisely to his or her needs. These include relative rate and ratio tests, several methods of ML based phylogeny reconstruction, bootstrapping, model selection, positive selection, molecular clock tests and many more

::DEVELOPER

Acme Computational Molecular Evolution Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux

:: DOWNLOAD

  HyPhy

:: MORE INFORMATION

Citation

Sergei L. Kosakovsky Pond, Simon D. W. Frost and Spencer V. Muse (2005)
HyPhy: hypothesis testing using phylogenies.
Bioinformatics 21(5): 676-679

taxator-tk 1.3.3 – Taxonomic Sequence Assignment

taxator-tk 1.3.3

:: DESCRIPTION

taxator-tk is an algorithm and the accompanying software, which performs taxonomic sequence assignment by fast approximate determination of evolutionary neighbors from sequence similarities.

::DEVELOPER

Algorithmic Bioinformatics, Heinrich-Heine-Universität Düsseldorf

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 taxator-tk

:: MORE INFORMATION

Citation

Taxator-tk: Precise Taxonomic Assignment of Metagenomes by Fast Approximation of Evolutionary Neighborhoods.
Dröge J, Gregor I, McHardy AC.
Bioinformatics. 2014 Nov 10. pii: btu745.

simRRLs 1.5 – Simulate fastQ formatted RAD, ddRAD or GBS data on a fixed Species Tree

simRRLs 1.5

:: DESCRIPTION

The script simRRLs.py can be used to simulate RADseq-like sequences on a fixed species tree under a coalescent model. See Example usage page for advanced options, including simulating missing data, indels and different levels of divergence between taxa.

::DEVELOPER

Deren Eaton

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Python

:: DOWNLOAD

 simRRLs

:: MORE INFORMATION

mesquite 3.6.1 – Modular System for Evolutionary Analysis

mesquite 3.6.1

:: DESCRIPTION

Mesquite is software for evolutionary biology, designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses available depend on the modules installed.

::DEVELOPER

Mesquite team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX

:: DOWNLOAD

mesquite

:: MORE INFORMATION

Citation

W P Maddison, D R Maddison
Mesquite: A modular system for evolutionary analysis
Evolution (2008) Volume: 62, Issue: 5,Pages: 1103-1118

PhyML 2020 – Phylogeny software based on the Maximum Likelihood

PhyML 2020

:: DESCRIPTION

PhyML (Phylogenetic estimation using Maximum Likelihood) is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm to perform Nearest Neighbor Interchanges (NNIs), in order to improve a reasonable starting tree topology.

PhyML Online Version

::DEVELOPER

Stéphane GuindonOlivier Gascuel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

PhyML

:: MORE INFORMATION

Citation:

Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O.
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
Systematic Biology, 59(3):307-21, 2010.

BMGE 1.12 – Selection of Phylogenetic Informative Regions from Multiple Sequence Alignments

BMGE 1.12

:: DESCRIPTION

BMGE (Block Mapping and Gathering using Entropy) is a program that selects regions in a multiple sequence alignment that are suited for phylogenetic inference.

::DEVELOPER

BMGE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • Java

:: DOWNLOAD

 BMGE

:: MORE INFORMATION

Citation

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments.
Criscuolo A, Gribaldo S.
BMC Evol Biol. 2010 Jul 13;10:210. doi: 10.1186/1471-2148-10-210.

pez 1.2-3 – Phylogenetics for the Environmental Sciences

pez 1.2-3

:: DESCRIPTION

pez is an R package that permits measurement, modelling, and simulation of phylogenetic structure in ecological data

::DEVELOPER

the Pearse Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • R

:: DOWNLOAD

 pez

:: MORE INFORMATION

Citation

pez: Phylogenetics for the Environmental Sciences.
Pearse WD, Cadotte M, Cavender-Bares J, Ives AR, Tucker C, Walker S, Helmus MR.
Bioinformatics. 2015 May 5. pii: btv277.

Vizardous 1.2.0 – Analysis of Microbial Populations with Single Cell Resolution

Vizardous 1.2.0

:: DESCRIPTION

Vizardous is a software for the visualization and evaluation of time-resolved, quantitative, single-cell data.

::DEVELOPER

Modeling & Simulation group at the IBG-1

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 Vizardous

:: MORE INFORMATION

Citation

Vizardous: interactive analysis of microbial populations with single cell resolution.
Helfrich S, Azzouzi CE, Probst C, Seiffarth J, Grünberger A, Wiechert W, Kohlheyer D, Nöh K.
Bioinformatics. 2015 Aug 10. pii: btv468

PAML 4.8a / PAMLX 1.3.1 – Phylogenetic Analysis by Maximum Likelihood

PAML 4.8a / PAMLX 1.3.1

:: DESCRIPTION

PAML (Phylogenetic Analysis by Maximum Likelihood) is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood.The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (dN and dS) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations. This note discusses some of the major applications of the package, which includes example data sets to demonstrate their use.

PAML-X: A GUI for PAML

::DEVELOPER

Ziheng Yang

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

PAML , PAML-X

:: MORE INFORMATION

Citation:

Yang, Z. 2007.
PAML 4: a program package for phylogenetic analysis by maximum likelihood.
Molecular Biology and Evolution 24: 1586-1591

Mol Biol Evol. 2013 Oct 24.
PAMLX: A Graphical User Interface for PAML.
Xu B, Yang Z.

ArboDraw 2006 – Phylogenetic Tree Builder & Viewer

ArboDraw 2006

:: DESCRIPTION

ArboDraw is a program for building and displaying phylogenetic trees of protein and nucleic acid sequences. It can import and display dendrogram files in Newick format (generated by MUSCLE, Phylip, clustalw, etc.). Among the key features are the ability to annotate sequences, and to select and color independently various parts of the tree. A very convenient annotation functionality allows the user to view annotations by placing the mouse above the sequence of interest. Edited and annotated files can be saved and restored at a later time.

::DEVELOPER

Dunbrack Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

ArboDraw

:: MORE INFORMATION

For comments, suggestions and bug reports contact the authors: