Treevolution 1.2 – Visual Analysis of Phylogenetic Trees

Treevolution 1.2

:: DESCRIPTION

Treevolution is a Java tool for the representation and exploration of phylogenetic trees that facilitates visual analysis. There are several useful tools to visualize phylogenetic trees, but their level of interaction is usually low, especially in the case of radial representations. Highly interactive visualizations can improve the exploration and understanding of phylogenetic trees. Treevolution implements strategies to interact with phylogenetic trees in order to allow a more thorough analysis by users.

::DEVELOPER

The VisUsal (Visual Analytics and Information Visualization, Universidad de Salamanca) group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

Treevolution

:: MORE INFORMATION

Citation

Santamaría R. and Therón, R.
Treevolution: visual analysis of phylogenetic trees.
Bioinformatics, 2009, 25, 1970-1971

Ktreedist 1.0 – Calculation of the Minimum Branch Length Distance (K tree score) between Phylogenetic Trees

Ktreedist 1.0

:: DESCRIPTION

Ktreedist is a computer program written in Perl that calculates the minimum branch length distance from one phylogenetic tree to another, providing a measure of the difference in topology and relative branch lengths (shape) between two trees

::DEVELOPER

Castresana Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Perl

:: DOWNLOAD

 Ktreedist

:: MORE INFORMATION

Citation:

Soria-Carrasco, V., Talavera, G., Igea, J., and Castresana, J. (2007).
The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees.
Bioinformatics 23, 2954-2956.

SICLE 1.2 – high-throughput tool for Extracting Evolutionary Relationships from Phylogenetic Trees

SICLE 1.2

:: DESCRIPTION

SICLE (Sister Clade Extractor) is an easy to use, adaptable, and high-throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship.

::DEVELOPER

Dr. Dan DeBlasio

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 SICLE

:: MORE INFORMATION

Citation

SICLE: A high-throughput tool for extracting evolutionary relationships from phylogenetic trees
Dan DeBlasio, Jennifer Wiscaver
Genomics arXiv:1303.5785

SSA 1.0 – Inference of Maximum Likelihood Phylogenetic Trees Using a Stochastic Search Algorithm

SSA 1.0

:: DESCRIPTION

SSA is a program for inferring maximum likelihood phylogenies from DNA sequences. Two versions of the program are available: one which assumes a molecular clock and one which does not make this assumption. The method for searching the space of trees for the ML tree is based on a simulated-annealing type algorithm and is described in the reference above. The program implements Felsenstein’s F84 model of nucleotide substitution and associated sub-models. The program estimates the ML tree and branch lengths, and can optionally estimate the transversion/transversion ratio. Upon termination, the program returns the k trees of highest likelihood found during the search, where k can be set by the user.

::DEVELOPER

Laura S. Kubatko

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 SSA

:: MORE INFORMATION

Citation

Salter, L. and D. Pearl. 2001.
Stochastic Search Strategy for Estimation of Maximum Likelihood Phylogenetic Trees,
Systematic Biology 50(1): 7-17.

SSAMK – Inference of Maximum Likelihood Phylogenetic Trees for Morphological Data

SSAMK

:: DESCRIPTION

SSAMK uses a stochastic search algorithm for estimation of maximum likelihood phylogenetic trees for morphological data

::DEVELOPER

Laura S. Kubatko

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SSAMK

:: MORE INFORMATION

Citation

Syst Biol. 2001 Nov-Dec;50(6):913-25.
A likelihood approach to estimating phylogeny from discrete morphological character data.
Lewis PO.

MY-CLOSURE 1.0 – Computing a Phylogenetic Network from a collection of Phylogenetic Trees

MY-CLOSURE 1.0

:: DESCRIPTION

MY-CLOSURE is a Java program for computing a phylogenetic network from a collection of phylogenetic trees.

::DEVELOPER

The UEA Computational Biology Laboratory at the University of East Anglia (UEA)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java

:: DOWNLOAD

 MY-CLOSURE

:: MORE INFORMATION

Citation

S. Grunewald, K. T. Huber and Q. Wu,
2 Novel Closure Rules for Constructing Phylogenetic Super-networks,
Bulletin of Mathematical Biology, 70: 1906-1924, 2008

TreeLign / FastTreeLign – Automatic update of 16s rRNA Phylogenetic Tree and Multiple Sequence Alignment in Metagenomics

TreeLign / FastTreeLign

:: DESCRIPTION

TreeLign is automatic update of 16s rRNA phylogenetic tree and multiple sequence alignment in metagenomics

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler
  • Perl

:: DOWNLOAD

 TreeLign

:: MORE INFORMATION

FitchAln 20100321 – Given Phylogenetic Tree and Multiple Sequence Alignment, show the Fitch Score Matrix

FitchAln 20100321

:: DESCRIPTION

Given a newick binary tree T and its correpsonding multiple sequence alignemnt A of size n x m, where n is the number of leaf nodes in T and m is the length of the alignment, FitchAln generates a (n-1) x (m+1) Fitch score matrix representing the (Maximum Parsimony) number of mutations for each site for each internal node.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 FitchAln

:: MORE INFORMATION

SDBP 1.0 – Assessing Statistical Reliability of Phylogenetic Trees

SDBP 1.0

:: DESCRIPTION

SDBP (speedy double bootstrap probability) is R package for assenssing the statistical reliability of phylogenetic trees.

::DEVELOPER

Akiyama Laboratory, Tokyo Institute of Technology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R package
:: DOWNLOAD

  SDBP

:: MORE INFORMATION

Citation

Ren, A., Ishida, T. and Akiyama, Y., 2013.
Assessing statistical reliability of phylogenetic trees via a speedy double bootstrap method
Molecular Phylogenetic of evolutionm, 67(2), 429-435. doi:10.1016/j.ympev.2013.02.011