Tag: Phylogenetic Tree

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

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.

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.

nhPhyML – Compute Phylogenetic Trees under non Homogeneous model of DNA sequence Evolution

nhPhyML

:: DESCRIPTION

nhPhyML is a program built to compute phylogenetic trees under the non stationary, non homogeneous model of DNA sequence evolution of Galtier and Gouy (1998).

::DEVELOPER

Bastien Boussau

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Mac OsX

:: DOWNLOAD

  nhPhyML

:: MORE INFORMATION

Citation

Efficient likelihood computations with nonreversible models of evolution.
Boussau B, Gouy M.
Syst Biol. 2006 Oct;55(5):756-68.

Xscape – Tools for Maximum-Parsimony Phylogenetic Tree Reconciliation over the Event Cost Landscape

Xscape

:: DESCRIPTION

Xscape is a set of Python tools for maximum parsimony phylogenetic event-based tree reconciliation in undated trees using the DTL (duplication-loss-transfer) model with applications to gene trees and species trees; parasite trees and host trees; and species trees and area cladograms.

::DEVELOPER

Ran Libeskind-Hadas

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • Python
  • matplotlib
  • BioPython

:: DOWNLOAD

 Xscape

:: MORE INFORMATION

Citation

Pareto-optimal phylogenetic tree reconciliation.
Libeskind-Hadas R, Wu YC, Bansal MS, Kellis M.
Bioinformatics. 2014 Jun 15;30(12):i87-i95. doi: 10.1093/bioinformatics/btu289.

TreeSAAP 3.2 – Selection of Amino Acid Properties using Phylogenetic Trees model

TreeSAAP 3.2

:: DESCRIPTION

TreeSAAP (Selection of Amino Acid Properties Based on Phylogenetic Trees) measures the selective influences on 31 structural and biochemical amino acid properties during phylogenesis (the history of genealogical development) and performs goodness-of-fit and categorical statistical tests.

::DEVELOPER

McClellan, David

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux

:: DOWNLOAD

TreeSAAP

:: MORE INFORMATION

Citation

TreeSAAP: selection on amino acid properties using phylogenetic trees.
Woolley S, Johnson J, Smith MJ, Crandall KA, McClellan DA.
Bioinformatics. 2003 Mar 22;19(5):671-2

FigTree 1.4.4 – Produce Figures of Phylogenetic Trees

FigTree 1.4.4

:: DESCRIPTION

FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures. In particular it is designed to display summarized and annotated trees produced by BEAST.

::DEVELOPER

Andrew Rambaut Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOS
  • Java

:: DOWNLOAD

FigTree

:: MORE INFORMATION

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EvolView v3 – An Online Phylogenetic Tree Viewer and Customization Tool

EvolView v3

:: DESCRIPTION

EvolView is an easy-to-use online tool for displaying, managing and customizing phylogenetic trees.

::DEVELOPER

EvolView team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 EvolView

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2019 Jul 2;47(W1):W270-W275. doi: 10.1093/nar/gkz357.
Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees.
Subramanian B, Gao S, Lercher MJ, Hu S, Chen WH.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W569-72. doi: 10.1093/nar/gks576. Epub 2012 Jun 13.
EvolView, an online tool for visualizing, annotating and managing phylogenetic trees.
Zhang H1, Gao S, Lercher MJ, Hu S, Chen WH

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