PAL 1.5.1 – Java Library for Molecular Evolution & Phylogenetics

PAL 1.5.1

:: DESCRIPTION

PAL (Phylogenetic Analysis Library) project is a collaborative effort to provide a high quality Java library for use in molecular evolution and phylogenetics. Updates of PAL are released in regular intervals. At present (version 1.4) PAL consists of approximately 200 public classes/interfaces in 16 packages with a total of more than 35,000 lines of Java code.

::DEVELOPER

PAL Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

PAL

:: MORE INFORMATION

Citation

Drummond, A., and K. Strimmer. 2001.
PAL: An object-oriented programming library for molecular evolution and phylogenetics.
Bioinformatics 17: 662-663.

ivy – Interactive Visual Phylogenetics

ivy

:: DESCRIPTION

ivy is a Python module for the analysis and exploration of phylogenetic trees and comparative data.It is built on a powerful foundation of open-source software components, including numpy, scipy, matplotlib, and IPython.

::DEVELOPER

Richard Ree

:: SCREENSHOTS

ivy

:: REQUIREMENTS

  • Linux / Windows/MacOsX
  • Python
  • numpy, scipy, matplotlib, and IPython

:: DOWNLOAD

  ivy

:: MORE INFORMATION

PrIME 1.0.5 – Library and Accompanying tools for Phylogenetics

PrIME 1.0.5

:: DESCRIPTION

PrIME (Probabilistic Integrated Models of Evolution) is a library and accompanying tools for phylogenetics. PrIME mainly relies on Markov-chain Monte Carlo (MCMC) framework and probabilistic modeling.

::DEVELOPER

Ikram Ullah

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PrIME

:: MORE INFORMATION

Citation:

Integrating Sequence Evolution into Probabilistic Orthology Analysis.
Ullah I, Sjöstrand J, Andersson P, Sennblad B, Lagergren J.
Syst Biol. 2015 Nov;64(6):969-82. doi: 10.1093/sysbio/syv044

pez 1.1-0 – Phylogenetics for the Environmental Sciences

pez 1.1-0

:: DESCRIPTION

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

::DEVELOPER

William D. Pearse; will.pearse@gmail.com.

:: 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.

APE 3.3 – Analysis of Phylogenetics and Evolution

APE 3.3

:: DESCRIPTION

APE (Analysis of Phylogenetics and Evolution) is a package for the analysis of phylogenetics and evolution.APE provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, analyses of diversification and macroevolution, computing distances from allelic and nucleotide data, reading nucleotide sequences, and several tools such as Mantel’s test, computation of minimum spanning tree, generalized skyline plots, estimation of absolute evolutionary rates and clock-like trees using mean path lengths, non-parametric rate smoothing and penalized likelihood. Phylogeny estimation can be done with the NJ, BIONJ, and ME methods.

::DEVELOPER

APE Team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 APE

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Jun 1;28(11):1536-7. doi: 10.1093/bioinformatics/bts184. Epub 2012 Apr 11.
ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R.
Popescu AA1, Huber KT, Paradis E.

Paradis E., Claude J. & Strimmer K. 2004.
APE: analyses of phylogenetics and evolution in R language.
Bioinformatics 20: 289–290.

GeLL 2.0 – General Likelihood Library for use in Phylogenetics

GeLL 2.0

:: DESCRIPTION

GeLL is a General Likelihood Library for use in phylogenetics. It is intended to provide classes that facilitate investigating new models and techniques.

::DEVELOPER

Daniel Money

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows / Linux
  • JRE

:: DOWNLOAD

 GeLL

:: MORE INFORMATION

Citation

GeLL: A Generalized Likelihood Library for Phylogenetic Models.
Money D, Whelan S.
Bioinformatics. 2015 Feb 27. pii: btv126.

DrawTree-NDVP 1.0 – Phylogenetics software based on Normalized Descriptor Vector of Protein Sequence

DrawTree-NDVP 1.0

:: DESCRIPTION

DrawTree-NDVP (Draw Polytree) is a phylogenetics software based on normalized descriptor vector of proteins.

::DEVELOPER

Yuhua Yao

:: SCREENSHOTS

DrawTree-NDVP

:: REQUIREMENTS

  • Windows
  • MatLab

:: DOWNLOAD

 DrawTree-NDVP

:: MORE INFORMATION

fastphylo 1.0.1 – Fast tools for Phylogenetics

fastphylo 1.0.1

:: DESCRIPTION

fastphylo is a software package containing implementations of efficient algorithms for two common problems in phylogenetics: estimating DNA/protein sequence distances and reconstructing a phylogeny from a distance matrix.

::DEVELOPER

fastphylo team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • C++ Compiler

:: DOWNLOAD

 fastphylo 

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Nov 20;14:334. doi: 10.1186/1471-2105-14-334.
Fastphylo: Fast tools for phylogenetics.
Khan MA, Elias I, Sjölund E, Nylander K, Guimera RV, Schobesberger R, Schmitzberger P, Lagergren J, Arvestad L.

MLTreeMap 2.061 – Phylogenetics and Functionalities of Metagenomes

MLTreeMap 2.061

:: DESCRIPTION

MLTreeMap is a tool that employs full maximum likelihood to give insights into phylogenetic and functional properties of metagenomes and the underlying microbial communities. It does so by detecting and phylotyping a series of relevant marker genes on the submitted DNA fragments. Among these genes are protein coding phylogenetic markers, SSU rRNA genes and markers for important functional pathways.

::DEVELOPER

Christian von Mering (mering@imls.uzh.ch)

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • Blast
  • Gblocks

:: DOWNLOAD

 MLTreeMap

:: MORE INFORMATION

Citation

MLTreeMap–accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies.
Stark M, Berger SA, Stamatakis A, von Mering C.
BMC Genomics. 2010 Aug 5;11:461. doi: 10.1186/1471-2164-11-461.

PhyBayes 200208 – Bayesian Inference in Phylogenetics

PhyBayes 200208

:: DESCRIPTION

PhyBayes is a program for Bayesian inference in phylogenetics

– estimation of divergence dates / rates of molecular evolution
– Bayes factor and test of evolutionary hypotheses
– tree space search and estimation of the posterior probabilities
– estimation of heterogeneities in a data set (still a project…)

::DEVELOPER

The Aris-Brosou lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / DOS

:: DOWNLOAD

 PhyBayes

:: MORE INFORMATION

Citaion

Aris-Brosou, S. and Z. Yang. 2002.
The effects of models of rate evolution on estimation of divergence dates with a special reference to the metazoan 18S rRNA phylogeny.
Syst. Biol. 51:703-714.