IQ-TREE 1.4.2 / W-IQ-TREE – Efficient Phylogenetic Tree Reconstruction and ultrafast Bootstrap Approximation

IQ-TREE 1.4.2 / 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

ETE 3 – Python Environment for Phylogenetic Tree Exploration

ETE 3

:: 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  in the Centre for Genomic Regulation (Barcelona, Spain).

:: 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.

Archaeopteryx 0.9901 beta – Visualization, Analysis & Editing of Phylogenetic Trees

Archaeopteryx 0.9901 beta

:: 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 M Zmasek, Eddy lab

:: 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.

TREEFINDER 201103 – Computes Phylogenetic Trees from Molecular Sequences

TREEFINDER 201103

:: DESCRIPTION

TREEFINDER computes phylogenetic trees from molecular sequences.

::DEVELOPER

Gangolf Jobb

:: SCREENSHOTS

treefinder

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • JRE

:: DOWNLOAD

 TREEFINDER

:: MORE INFORMATION

Citation

Jobb, G., A. von Haeseler, and K. Strimmer.
TREEFINDER: A powerful graphical analysis environment for molecular phylogenetics
BMC Evol Biol. 2004 Jun 28;4:18.

SylvX 1.3 – A Viewer for Phylogenetic Tree Reconciliations

SylvX  1.3

:: DESCRIPTION

SylvX is a reconciliation viewer which implements classical phylogenetic graphic operators (swapping, highlighting, etc.) and new methods to ease interpretation and comparison of reconciliations (multiple maps, moving, shrinking sub-reconciliations).

::DEVELOPER

The Computational Biology Institute (IBC)

:: SCREENSHOTS

SylvX

:: REQUIREMENTS

  • Windows/ MacOsX

:: DOWNLOAD

  SylvX

:: MORE INFORMATION

Citation

SylvX: a viewer for phylogenetic tree reconciliations.
Chevenet F, Doyon JP, Scornavacca C, Jacox E, Jousselin E, Berry V.
Bioinformatics. 2015 Oct 29. pii: btv625

markophylo 1.0.2 – Markov Chain Models for Phylogenetic Trees

markophylo 1.0.2

:: DESCRIPTION

markophylo allows for fitting of maximum likelihood models using Markov chains on phylogenetic trees for analysis of discrete character data.

::DEVELOPER

Utkarsh J. Dang <udang at mcmaster.ca>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 markophylo

:: MORE INFORMATION

Citation

markophylo: Markov Chain Analysis on Phylogenetic Trees.
Dang UJ, Golding GB.
Bioinformatics. 2015 Sep 11. pii: btv541.

tax2tree 1.0 – Decorating Taxonomy onto a Phylogenetic tree

tax2tree 1.0

:: DESCRIPTION

tax2tree is a tool for automatically decorating taxonomy onto a phylogenetic tree. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.

::DEVELOPER

Knight Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Python
  • PyCogent

:: DOWNLOAD

 tax2tree

:: MORE INFORMATION

Citation

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea.
Daniel McDonald, Morgan N Price, Julia Goodrich, Eric P Nawrocki, Todd Z DeSantis, Alexander Probst, Gary L Andersen, Rob Knight and Philip Hugenholtz.
ISME J. 2012 Mar;6(3):610-8. doi: 10.1038/ismej.2011.139. Epub 2011 Dec 1.

TopiaryExplorer 1.0 – Interactive Phylogenetic Tree Viewing software

TopiaryExplorer 1.0

:: DESCRIPTION

TopiaryExplorer supports visualization of very large trees (it has been tested on trees with > 100,000 tips) while providing convenient interfaces for decorating the tree with taxonomic information, automatically coloring branches based on data about environments where they are observed, selecting subtrees for independent analysis, interactive expanding and collapsing of clades, and many other features.

::DEVELOPER

Knight Lab

:: SCREENSHOTS

TopiaryExplorer

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Java

:: DOWNLOAD

 TopiaryExplorer

:: MORE INFORMATION

Citation

Pirrung, M., R. Kennedy, J. G. Caporaso, J. Stombaugh, D. Wendel, and R. Knight. 2011.
TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata.
Bioinformatics 27, no. 21 (October 21): 3067–3069. http://dx.doi.org/10.1093/bioinformatics/btr517.

ggtree 1.1.16 – Phylogenetic Tree Viewer for Different Types of Tree Annotations

ggtree 1.1.16

:: DESCRIPTION

ggtree is a phylogenetic tree viewer for different types of tree annotations

::DEVELOPER

Guangchuang YU,

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • R
  • Bioconductor

:: DOWNLOAD

 ggtree

:: MORE INFORMATION

Citation:

Yu G (2015).
“ggtree: a phylogenetic tree viewer for different types of tree annotations.”
submitted.

RAxML 8.2.3 / RAxML Workbench 1.0 – Sequential and Parallel Maximum Likelihood based inference of large phylogenetic trees

RAxML 8.2.3 / RAxML Workbench 1.0

:: DESCRIPTION

RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein’s dnaml which is part of the PHYLIP package.

RAxML Workbench is a gaphical User Interface for the RAxML Evolutionary Placement Algorithm

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  RAxML , RAxML Workbench

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 1;30(9):1312-3. doi: 10.1093/bioinformatics/btu033. Epub 2014 Jan 21.
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
Stamatakis A.

S.A. Berger, D. Krompaß, A. Stamatakis:
Performance, Accuracy and Web-Server for Evolutionary Placement of Short Sequence Reads under maximum-likelihood“.
Systematic Biology 60(3):291-302, 2011.