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:

Consel 0.20 – Assess Confidence of Phylogenetic Tree Selection

Consel 0.20

:: DESCRIPTION

CONSEL is a program package consists of small programs written in C language. It calculates the probability value (i.e., p-value) to assess the confidence in the selection problem. Although CONSEL is applicable to any selection problem, it is mainly designed for the phylogenetic tree selection. CONSEL does not estimate the phylogenetic tree by itself, but CONSEL does read the output of the other phylogenetic packages, such as Molphy, PAML, PAUP*, TREE-PUZZLE, and PhyML. CONSEL calculates the p-value using several testing procedures; the bootstrap probability, the Kishino-Hasegawa test, the Shimodaira-Hasegawa test, and the weighted Shimodaira-Hasegawa test. In addition to these conventional tests, CONSEL calculates the p-value based on the approximately unbiased test using the multi-scale bootstrap technique.

::DEVELOPER

Hidetoshi Shimodaira

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows

:: DOWNLOAD

 CONSEL

:: MORE INFORMATION

Citation:

Shimodaira, H. & Hasegawa, M.
CONSEL: for assessing the confidence of phylogenetic tree selection.
Bioinformatics 17, 1246-1247 (2001).

MySSP 1.0.3.5 – Simulation of DNA Sequence Evolution across a Phylogenetic Tree

MySSP 1.0.3.5

:: DESCRIPTION

MySSP is a program for the simulation of DNA sequence evolution across a phylogenetic tree

::DEVELOPER

Michael S. Rosenberg’s Laboratory

:: SCREENSHOTS

MySSP

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MySSP

:: MORE INFORMATION

Citation

Rosenberg, M.S. (2005)
MySSP: Non-stationary evolutionary sequence simulation, including indels.
Evolutionary Bioinformatics Online 1:81–83

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.

NJplot 2.4 – Phylogenetic Tree Drawing Program

NJplot 2.4

:: DESCRIPTION

NJplot is a tree drawing program able to draw any phylogenetic tree expressed in the Newick phylogenetic tree format (e.g., the format used by the PHYLIP package). NJplot is especially convenient for rooting the unrooted trees obtained from parsimony, distance or maximum likelihood tree-building methods.

::DEVELOPER

PRABI-Doua

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX

:: DOWNLOAD

NJplot

:: MORE INFORMATION

Citation

Perrière, G. and Gouy, M. (1996)
WWW-Query: An on-line retrieval system for biological sequence banks.
Biochimie, 78, 364-369.

Unrooted – Draw Binary Tree Expressed in the standard Phylogenetic Tree Format

Unrooted

:: DESCRIPTION

Unrooted is a tree drawing program able to draw any binary tree expressed in the standard phylogenetic tree format (e.g., the format used by the PHYLIP package). Trees are drawn in an unrooted way, that is, using a circular shape, with labels aligned with terminal branches.

::DEVELOPER

Unrooted team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  Mac OsX / Windows

:: DOWNLOAD

 Unrooted

:: MORE INFORMATION

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.