Tag: Phylogenetic Tree

Archaeopteryx 0.9928 – Visualization, Analysis & Editing of Phylogenetic Trees

Archaeopteryx 0.9928

:: DESCRIPTION

Archaeopteryx is a software tool for the visualization, analysis, and editing of potentially large and highly annotated phylogenetic trees. Archaeopteryx (the successor to ATV) is entirely written in the Java programming language.

::DEVELOPER

Christian Zmasek

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

Archaeopteryx

:: MORE INFORMATION

Citation

Han M.V. and Zmasek C.M. (2009).
phyloXML: XML for evolutionary biology and comparative genomics.
BMC Bioinformatics, 10:356.

ETE 3.1.1 – Python Environment for Phylogenetic Tree Exploration

ETE 3.1.1

:: DESCRIPTION

ETE (Environment for Tree Exploration ) is a python programming toolkit that assists in the automated manipulation, analysis and visualization of phylogenetic and other type of trees. It provides a wide range of tree handling methods, node annotation features, programmatic access to the phylomeDB database, and automatic orthology and paralogy prediction methods. In addition, an interactive tree visualization program, as well as a highly customizable tree drawing engine, is included.

::DEVELOPER

Gabaldón’s lab

:: SCREENSHOTS

N/A

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ETE

:: MORE INFORMATION

Citation:

ETE 3: Reconstruction, analysis and visualization of phylogenomic data.
Huerta-Cepas J, Serra F, Bork P.
Mol Biol Evol. 2016 Feb 26. pii: msw046.

Jaime Huerta-Cepas*, Joaquín Dopazo and Toni Gabaldón*.
ETE: a python Environment for Tree Exploration.
BMC Bioinformatics 2010, 11:24.

TreeKO – Compare Phylogenetic Trees

TreeKO

:: DESCRIPTION

TreeKO is a python package used to compare phylogenetic trees

::DEVELOPER

Bioinformatics and Genomics @ CRG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/ Windows
  • Python

:: DOWNLOAD

 TreeKO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2011 May;39(10):e66. doi: 10.1093/nar/gkr087. Epub 2011 Feb 18.
TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees.
Marcet-Houben M, Gabaldón T.

IQ-TREE 1.6.12 / W-IQ-TREE – Efficient Phylogenetic Tree Reconstruction and ultrafast Bootstrap Approximation

IQ-TREE 1.6.12 / W-IQ-TREE

:: DESCRIPTION

IQ-TREE is a very efficient phylogenetic software for reconstructing maximum-likelihood trees and assessing branch supports with the ultrafast bootstrap approximation. It is based on the IQPNNI algorithm with 10-fold speedup together with substantially additional features.

W-IQ-TREE is an intuitive and user-friendly web interface and server for IQ-TREE

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX

:: DOWNLOAD

 IQ-TREE

:: MORE INFORMATION

Citation

W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis.
Trifinopoulos J, Nguyen LT, von Haeseler A, Minh BQ.
Nucleic Acids Res. 2016 Apr 15. pii: gkw256.

Bui Quang Minh, Minh Anh Thi Nguyen, and Arndt von Haeseler (2013)
Ultrafast approximation for phylogenetic bootstrap.
Mol. Biol. Evol.,doi: 10.1093/molbev/mst024

TreeSnatcher Plus 201206 – Phylogenetic Tree Capturing Tool

TreeSnatcher Plus 201206

:: DESCRIPTION

TreeSnatcher is a GUI-driven Java application that recognizes bifurcating and multifurcating trees in pixel images (like JPG) and outputs the tree in Newick format.

::DEVELOPER

Computational Cell Biology,   Heinrich-Heine-Universität Düsseldorf

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / WIndows /MacOsX
  • Java

:: DOWNLOAD

 TreeSnatcher

:: MORE INFORMATION

Citation:

Thomas Laubach, Arndt von Haeseler and Martin J. Lercher (2012),
TreeSnatcher Plus: Capturing Phylogenetic Trees from Images.
BMC Bioinformatics 2012, 13:110; DOI: 10.1186/1471-2105-13-110

Thomas Laubach and Arndt von Haeseler (2007),
TreeSnatcher: Coding Trees from Images.
Bioinformatics 2007 23(24):3384-338

SaffronTree v0.1.2 – Reference Free Rapid Phylogenetic Tree Construction from raw read data

SaffronTree v0.1.2

:: DESCRIPTION

SaffronTree takes FASTQ/FASTA files as input and uses a kmer analysis to build a phylogenetic neighbour joining tree in newick format.

::DEVELOPER

Pathogen Informatics, Wellcome Trust Sanger Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

SaffronTree

:: MORE INFORMATION

JTreeView 0.8 – Java based Phylogenetic Tree Viewer

JTreeView 0.8

:: DESCRIPTION

JTreeView is a basic tree viewer that lets you view, reroot, rotate nodes and edit further aspects of New Hampshire bracket format trees.

::DEVELOPER

JTreView team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

 JTreeView

:: MORE INFORMATION

TreeTest – Testing Phylogenetic Tree Topologies in a Frequentist Framework

TreeTest

:: DESCRIPTION

 TreeTest is a program for testing phylogenetic tree topologies in a frequentist framework.The software makes use of the baseml code (PAML), and implements tests of phylogenetic hypotheses (is the maximum likelihood tree the correct tree?) and significance tests.

::DEVELOPER

The Aris-Brosou lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

  TreeTest

:: MORE INFORMATION

Citaion

Aris-Brosou, S. 2003.
Least and most powerful phylogenetic tests to elucidate the origin of the seed plants in presence of conflicting signals under misspecified models.
Syst. Biol. 52:781-793

Phyrex 1.1 – Reconstruction of Continuous Character Trait Values at nodes of Phylogenetic Trees

Phyrex 1.1

:: DESCRIPTION

Phyrex (PHYlogenetic REconstruction by use of gene eXpression and alternate mRNA splicing patterns) is a program for reconstructing ancestral gene expression profiles and sequence data on a given phylogenetic tree. The program uses a Minimum Evolution algorithm to reconstruct the gene expression profiles and a combination of BaseML and ClustalW to reconstruct the ancestral sequences.

::DEVELOPER

Roald Rossnes

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • C++ Compiler

:: DOWNLOAD

 Phyrex

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2005 May 27;6:127.
Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.
Rossnes R, Eidhammer I, Liberles DA.

CTree 1.03 – Analysis of Clusters on Phylogenetic Trees

CTree 1.03

:: DESCRIPTION

 CTree has been designed for viewing, analyzing and editing phylogenetic trees. There is a particular emphasis on the analysis of clusters within such trees. Clusters are stored as individual data structures from which statistical data can be easily extracted.

::DEVELOPER

John Archer and David Robertson

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 CTree 

:: MORE INFORMATION

Citation

Archer J, Robertson DL.
CTree: comparison of clusters between phylogenetic trees made easy.
Bioinformatics (2007) 23 (21): 2952-2953.

Exit mobile version