Tag: Supertree

SDM – Fast Distance-based Approach for (Super)Tree Building in Phylogenomics

SDM

:: DESCRIPTION

SDM (super distance matrix ) is a new method to combine distance matrices (or trees with branch lengths). This method involves deforming the different matrices, without modifying their topological message, to bring them as close as possible to each other. A distance supermatrix is then computed by averaging the deformed source matrices. When this supermatrix is complete, any tree building algorithm can be used to obtain the supertree that summarizes the input distance matrices (or trees with branch lengths); e.g. BioNJ or FastME (recommended).

::DEVELOPER

Alexis Criscuolo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

 SDM

:: MORE INFORMATION

Citation

“SDM: a Fast Distance-based Approach for (Super)Tree Building in Phylogenomics.”
Criscuolo A., Berry V., Douzery E.J.P., Gascuel O.
Systematic Biology. 2006 55(5):740-755.

RFsupertrees 2.0 – Program for Constructing Accurate Supertrees

RFsupertrees 2.0

:: DESCRIPTION

RFsupertrees (Robinson-Foulds Supertrees) takes as input a collection of rooted trees and heuristically searches for a binary supertree that minimizes the total (rooted) Robinson-Foulds distance between the supertree and the input trees. The intuition behind seeking a binary supertree, even though the input trees may be non-binary (unresolved), is that, under this setting, minimizing the RF distance is equivalent to maximizing the number of shared clades (or clusters) between the input trees and the supertree. Thus, an RF supertree is a supertree that is consistent with the largest number of clusters from the input trees. The program can quickly compute accurate supertrees for even large datasets containing thousands of input trees with many hundreds of taxa.

::DEVELOPER

Computational Biology Laboratory, Department of Computer Science,Iowa State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

 RFsupertrees

:: MORE INFORMATION

Citation

Robinson-Foulds Supertrees
Mukul S. Bansal, J. G. Burleigh, Oliver Eulenstein, David Fernandez-Baca.
Algorithms for Molecular Biology 2010, 5:18.

Rainbow beta 1.2 – Toolbox for Phylogenetic Supertree Construction & Analysis

Rainbow beta 1.2

:: DESCRIPTION

Rainbow is a program that provides a graphic user interface to construct supertrees using different methods. It also provides tools to analyze the quality of the supertrees produced.

::DEVELOPER

Computational Biology Laboratory, Department of Computer Science , Iowa State University

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Rainbow

:: MORE INFORMATION

Citation

D. Chen, O. Eulenstein and D. Fernández-Baca
Rainbow: a toolbox for phylogenetic supertree construction and analysis
Bioinformatics (2004) 20 (16): 2872-2873.

SuperTriplets 1.1 – Triplet-based Supertree Approach to Phylogenomics

SuperTriplets 1.1

:: DESCRIPTION

SuperTriplets is a triplet-based supertree approach to phylogenomics. It infers supertrees with branch support values.

::DEVELOPER

SuperTriplets team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 SuperTriplets

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jun 15;26(12):i115-23. doi: 10.1093/bioinformatics/btq196.
SuperTriplets: a triplet-based supertree approach to phylogenomics.
Ranwez V1, Criscuolo A, Douzery EJ.

SuperFine – Supertree Estimation

SuperFine

:: DESCRIPTION

SuperFine is software for constructing supertrees from source phylogenies.

::DEVELOPER

The Warnow Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows/MacOsX
  • Python

:: DOWNLOAD

 SuperFine

:: MORE INFORMATION

Citation:

SuperFine: fast and accurate supertree estimation.
Swenson MS, Suri R, Linder CR, Warnow T.
Syst Biol. 2012 Mar;61(2):214-27. doi: 10.1093/sysbio/syr092.

Clann 4.2.5 – Construct Phylogenetic Supertrees

Clann 4.2.5

:: DESCRIPTION

Clann (the Irish word for “family”), is a free software program designed and written by Chris Creevey at the Bioinformatics and Pharmacogenomics Laboratory at NUI Maynooth. The purpose of the program is to implement methods of determining the optimal phylogenetic supertree, given a set of input source trees.

::DEVELOPER

McInerney lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

Clann

:: MORE INFORMATION

Citation:

Creevey C. J. and McInerney, J. O. 2005
Clann: Investigating phylogenetic information through supertree analyses.
Bioinformatics 21 (3): 390-2.

mrc.py 1.0 – Compatibility Lengths of Supertrees and Gene Trees

mrc.py 1.0

:: DESCRIPTION

MRC.py is a computer program to evaluate the compatibility lengths given supertrees and gene trees and to extract the supertrees with the minimal lengths

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 MRC.py

:: MORE INFORMATION