MALT 0.4.1 – MEGAN Alignment tool

MALT 0.4.1

:: DESCRIPTION

MALT performs alignment of metagenomic reads against a database of reference sequences (such as NR, GenBank or Silva) and produces a MEGAN RMA file as output.

::DEVELOPER

the Algorithms in Bioinformatics lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

MALT

:: MORE INFORMATION

LibSBGN Milestone 3.2 – Standard Electronic Implementation for SBGN

LibSBGN Milestone 3.2

:: DESCRIPTION

LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format.

::DEVELOPER

LibSBGN team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

 LibSBGN

:: MORE INFORMATION

Citation

Software support for SBGN maps: SBGN-ML and LibSBGN.
van Iersel MP, Villéger AC, Czauderna T, Boyd SE, Bergmann FT, Luna A, Demir E, Sorokin A, Dogrusoz U, Matsuoka Y, Funahashi A, Aladjem MI, Mi H, Moodie SL, Kitano H, Le Novère N, Schreiber F.
Bioinformatics. 2012 Aug 1;28(15):2016-21. Epub 2012 May 10.

AlgorithmTreeFromLabels 1.0 – Creat Nexus files from Classificatory Language labels

AlgorithmTreeFromLabels 1.0

:: DESCRIPTION

AlgorithmTreeFromLabels takes as input a set of classificatory labels and creates a file in a format which can be loaded into Splitstree such that the corresponding phylogeny can be viewed and analyzed.

::DEVELOPER

The ASJP project

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Python

:: DOWNLOAD

 AlgorithmTreeFromLabels

:: MORE INFORMATION

References
Huson, D. H. and D. Bryant. 2006. Application of phylogenetic networks in evolutionary
studies. Mol. Biol. Evol. 23(2): 254-267.

MEGAN 6.18.0 – Metagenome analysis

MEGAN 6.18.0

:: DESCRIPTION

MEGAN (MEta Genome ANalyzer) allows laptop analysis of large metagenomic data sets. In a preprocessing step, the set of DNA sequences is compared against databases of known sequences using BLAST or another comparison tool. MEGAN is then used to compute and explore the taxonomical content of the data set, employing the NCBI taxonomy to summarize and order the results. A simple lowest common ancestor algorithm assigns reads to taxa such that the taxonomical level of the assigned taxon reflects the level of conservation of the sequence. The software allows large data sets to be dissected without the need for assembly or the targeting of specific phylogenetic markers. It provides graphical and statistical output for comparing different data sets.

::DEVELOPER

the Algorithms in Bioinformatics lab.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

 MEGAN

:: MORE INFORMATION

Citation

Analysis of 16S rRNA environmental sequences using MEGAN.
Mitra S, Stärk M, Huson DH.
BMC Genomics. 2011 Nov 30;12 Suppl 3:S17. doi: 10.1186/1471-2164-12-S3-S17.

SplitsTree 4.15.1 – Compute Phylogenetic Networks

SplitsTree 4.15.1

:: DESCRIPTION

SplitsTree uses the split decomposition method to analyse and visualize distance data, e.g. data derived from biosequences. SplitsTree4 is the leading application for computing unrooted phylogenetic networks from molecular sequence data. Given an alignment of sequences, a distance matrix or a set of trees, the program will compute a phylogenetic tree or network using methods such as split decomposition, neighbor-net, consensus network, super networks methods or methods for computing hybridization or simple recombination networks.

::DEVELOPER

the Algorithms in Bioinformatics lab.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX

:: DOWNLOAD

SplitsTree

:: MORE INFORMATION

Citation

D. H. Huson and D. Bryant,
Application of Phylogenetic Networks in Evolutionary Studies
Mol. Biol. Evol., 23(2):254-267, 2006.

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

Dendroscope 3.6.3 – Visualize Phylogenetic Trees & Rooted Networks

Dendroscope 3.6.3

:: DESCRIPTION

Dendroscope is a software for the interactive visualization and navigation of phylogenetic trees. The program provides all standard tree visualizations and is optimized to run interactively on trees containing hundreds of thousands of taxa. The program provides tree editing and graphics export capabilities. To support the inspection of large trees, Dendroscope offers a magnification tool.

::DEVELOPER

the Algorithms in Bioinformatics lab.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

Dendroscope

:: MORE INFORMATION

Citation:

Daniel H Huson, Daniel C Richter, Christian Rausch, Tobias Dezulian, Markus Franz and Regula Rupp.
Dendroscope: An interactive viewer for large phylogenetic trees,
BMC Bioinformatics. 2007 Nov 22;8(1):460

TreeTime 1.0.1 – Bayesian Sampling of Phylogenetic Trees from Molecular data

TreeTime 1.0.1

:: DESCRIPTION

TreeTime is an extensible C++ software package for the Bayesian sampling of phylogenetic trees from molecular data.

::DEVELOPER

Lin Himmelmann

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/MacOsX

:: DOWNLOAD

 TreeTime

:: MORE INFORMATION

Citation

TreeTime: an extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration.
Himmelmann L, Metzler D.
Bioinformatics. 2009 Sep 15;25(18):2440-1. doi: 10.1093/bioinformatics/btp417.

Baobab 3.31 – Editor for Large Phylogenetic Trees

Baobab 3.31

:: DESCRIPTION

Baobab is an editor for large phylogenetic trees written in Java. It allows you to create and/or modify a tree interactively, adding/(re)moving branches and nodes, changing leave names, setting parameters. Baobab focuses on edition, not representation and display that are only used as a tool to make edition easier.

::DEVELOPER

Dr Julien Y. Dutheil

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

Baobab

:: MORE INFORMATION

Citation:

Dutheil J, Galtier N.
BAOBAB: a Java editor for large phylogenetic trees.
Bioinformatics. 2002 Jun;18(6):892-3.

PhyML_Multi – Compute Phylogenetic Trees in cases where events of Homologous Recombination have Affected an Alignment

PhyML_Multi

:: DESCRIPTION

PhyML_Multi is a program built to compute phylogenetic trees in cases where events of homologous recombination have affected an alignment. It can simultaneously reconstruct phylogenetic trees and find recombination breakpoints.

::DEVELOPER

Bastien Boussau

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows/MacOsX
  • C++ Compiler

:: DOWNLOAD

 PhyML_Multi

:: MORE INFORMATION

Citation:

Boussau B, Guéguen L, Gouy M (2009).
A Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies“,
Evolutionary Bioinformatics, 2009, Jun 25;5:67-79.