RAP / RAP-Green – Phylogenetic Tree Reconciler

RAP / RapGreen

:: DESCRIPTION

RAP is an algorithm and a software have been developed, which permit to find gene duplications in phylogenetic trees, in order to improve gene function inferences. The algorithm is applicable to realistic data, especially n-ary species tree and unrooted phylogenetic tree

RAP-Green is a new implementation and an improvment of the RAP software which permits to compare gene and species trees, infers duplication events, and provide confidence score in function conservation between genes.

::DEVELOPER

South Green bioinformatics platform

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  Mac OsX / Windows
  • Java

:: DOWNLOAD

  RAP , RapGreen

:: MORE INFORMATION

Citation

Dufayard JF, Bocs S, Guignon V, Larivière D, Louis A, Oubda N, Rouard M, Ruiz M, de Lamotte F.
RapGreen, an interactive software and web package to explore and analyze phylogenetic trees.
NAR Genom Bioinform. 2021 Sep 23;3(3):lqab088. doi: 10.1093/nargab/lqab088. PMID: 34568824; PMCID: PMC8459725.

RΕQ 2.0 – Assessing branch supports of a Distance-based Phylogenetic Tree with the Rate of Elementary Quartets

RΕQ 2.0

:: DESCRIPTION

REQ is a command line program written in Java that estimates the rate of elementary quartets (REQ) for each internal branch of an unrooted binary phylogenetic tree from a distance matrix.

::DEVELOPER

Alexis Criscuolo (alexis.criscuolo@pasteur.fr)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

RΕQ 

:: MORE INFORMATION

PhyloSketch 0.1.8 – Sketch rooted Phylogenetic Trees and networks

PhyloSketch 0.1.8

:: DESCRIPTION

PhyloSketch is an interactive program for sketching rooted phylogenetic trees and networks. The program reports on some of mathematical properties of the network. The program can import and export rooted phylogenetic trees or networks in (extended) Newick format.

::DEVELOPER

the Algorithms in Bioinformatics lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

PhyloSketch

:: MORE INFORMATION

Dendroscope 3.7.6 – Visualize Phylogenetic Trees & Rooted Networks

Dendroscope 3.7.6

:: 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

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