mswordtree 1.0 – MS Word Macro for Drawing of Phylogenetic Trees

mswordtree 1.0

:: DESCRIPTION

mswordtree is a tool for generating graphical phylogenetic trees in a Microsoft Word document directly from a Newick format description. The resulting graphic is a Word picture and so can then be moved easily between MS Office applications and extensively edited. mswordtree is a Word Basic macro and can therefore be integrated directly into your installation of Word, eliminating the need for an external program to graphically render your trees.

::DEVELOPER

DICKS COMPUTATIONAL BIOLOGY GROUP

:: SCREENSHOTS

:: REQUIREMENTS

Windows/ Mac OsX
MS Word

:: DOWNLOAD

mswordtree

:: MORE INFORMATION

Citation:

Savva G, Conn J and Dicks J (2004)
Drawing phylogenetic trees in LaTeX and Microsoft Word
Bioinformatics 20(14): 2322-2323.

CGHdist 1.0 – Calculates Mximum Likelihood-based Distances from Gene Content

CGHdist 1.0

:: DESCRIPTION

CGHdist is a phylogenetics program which estimates distance matrices based on gene content derived from the results of comparative genome hybridisation arrays. The method used is described in our paper (Savva et al) which is available for download.

::DEVELOPER

DICKS COMPUTATIONAL BIOLOGY GROUP

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux / Mac OsX

:: DOWNLOAD

CGHdist for Win ; Source Code

:: MORE INFORMATION

Contact the author at g.savva@qmul.ac.ukto report bugs, give comments and suggestions, or if you would like to be kept up to date with future releases / bug fixes.

MPI-PHYLIP – Parallelizing Computationally Intensive Phylogenetic Analysis

MPI-PHYLIP

:: DESCRIPTION

MPI-PHYLIP is a modified PHYLIP package using MPI to enable large-scale phylogenetic study of protein sequences, using a statistically robust number of bootstrapped datasets, to be performed in a moderate amount of time.

::DEVELOPER

National Resource for Biomedical Supercomputing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Mac OsX / Linux

:: DOWNLOAD

MPI-PHYLIP

:: MORE INFORMATION

Citation

Ropelewski AJ, Nicholas HB Jr, Gonzalez Mendez RR (2010)
MPI-PHYLIP: Parallelizing Computationally Intensive Phylogenetic Analysis Routines for the Analysis of Large Protein Families.
PLoS ONE 5(11): e13999. doi:10.1371/journal.pone.0013999

Leaphy 1.0 beta – Phylogenetic Tree Estimation Software

Leaphy 1.0 beta

:: DESCRIPTION

Leaphy (Likelihood Estimation Algorithms in Phylogenetics) uses maximum likelihood (ML) to estimate trees from aligned amino acid and nucleotide sequences under a variety of commonly used and popular models.

::DEVELOPER

Simon Whelan

:: REQUIREMENTS

Windows / Linux / MacOSX

:: DOWNLOAD

Leaphy

:: MORE INFORMATION

Citation

S. Whelan.
New approaches to phylogenetic tree search and their application to large numbers of protein alignments.
Syst Biol (2007) 56 (5): 727-740. doi: 10.1080/10635150701611134

TreeDyn 198.3 – Dynamic Graphics & Annotations for Phylogenetic Analyses

TreeDyn 198.3

:: DESCRIPTION

TreeDyn is a tool using annotations and dynamic graphical methods for editing and analyzing multiple trees. The main features of TreeDyn are 1) the management of multiple windows and multiple trees per window, 2) the export of graphics to several standard file formats with or without HTML encapsulation and a new format called TGF, which enables saving and restoring graphical analysis, 3) the projection of texts or symbols facing leaf labels or linked to nodes, through manual pasting or by using annotation files, 4) the highlight of graphical elements after querying leaf labels (or annotations) or by selection of graphical elements and information extraction, 5) the highlight of targeted trees according to a source tree browsed by the user, 6) powerful scripts for automating repetitive graphical tasks, 7) a command line interpreter enabling the use of TreeDyn through CGI scripts for online building of trees, 8) the inclusion of a library of packages dedicated to specific research fields involving trees.

::DEVELOPER

GEMI Bioinformatics F. Chevenet

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOsX / Linux

:: DOWNLOAD

TreeDyn

:: MORE INFORMATION

Citation:

Chevenet F., Brun C., Banuls A.L., Jacq B. and R. Christen
TreeDyn: towards dynamic graphics and annotations for analyses of trees
BMC Bioinformatics 2006, 7:439

CDTree 3.1 – Protein Domain Hierarchy Viewer and Editor

CDTree 3.1

:: DESCRIPTION

CDTree is a powerful tool to aid in the classification of protein sequences and investigate their evolutionary relationships;

::DEVELOPER

The NCBI Structure Group

:: SCREENSHOTS

:: REQUIREMENTS

Windows/MacOsX

:: DOWNLOAD

CDTree

:: MORE INFORMATION

Citation:

Marchler-Bauer A, Anderson JB, Derbyshire MK, DeWeese-Scott C, Gonzales NR, Gwadz M, Hao L, He S, Hurwitz DI, Jackson JD, Ke Z, Krylov D, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Thanki N, Yamashita RA, Yin JJ, Zhang D, Bryant SH.
CDD: a conserved domain database for interactive domain family analysis.
Nucleic Acids Res. 2007;35 (Database Issue):D237-40.

TreeMe 200807 – Visualization, Editing and Annotation of Phylogenetic Trees

TreeMe 200807

:: DESCRIPTION

TreeMe is a comprehensive phylogenetic tree visualization and manipulation software for phylogenetics and research in evolution.

::DEVELOPER

SequentiX – Digital DNA Processing

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

TreeMe

:: MORE INFORMATION

Purchasing TreeMe

TreeJuxtaposer 2.1 – View a Single Tree, or Compare Two or more Trees

TreeJuxtaposer 2.1

:: DESCRIPTION

TreeJuxtaposer lets you interactively view a single tree, or compare two or more trees. The software handles all kinds of trees, including phylogenetic trees, taxonomic trees, consensus trees, dendrograms from cluster hierarchies, and others. Uses nested parentheses (Newick/New Hampshire) data format. Guaranteed visibility of marked regions provides visual landmarks. Structural differences are automatically marked, and the marked clades highlight corresponding nodes on the trees through the use of a generalization of the Robinson-Foulds distance metric. Responsive drawing for even very large trees with advanced graphics techniques.

::DEVELOPER

TreeJuxtaposer Team

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOSX
Java

:: DOWNLOAD

TreeJuxtaposer

:: MORE INFORMATION

Citation:

Tamara Munzner, Francois Guimbretiere, Serdar Tasiran, Li Zhang, and Yunhong Zhou.
TreeJuxtaposer: Scalable Tree Comparison using Focus+Context with Guaranteed Visibility
Proc. SIGGRAPH 2003, published as ACM Transactions on Graphics 22(3), pages 453–462

TreeEdit 1.0a10 – Organize, View & Manipulate sets of Phylogenetic Trees

TreeEdit 1.0a10

:: DESCRIPTION

TreeEdit is an easy to use application for organizing, viewing and manipulating sets of phylogenetic trees. TreeEdit is intended as a tool for preparing sets of trees for use in phylogenetics packages such as PAUP.

::DEVELOPER

Andrew Rambaut Group

:: SCREENSHOTS

:: REQUIREMENTS

MacOSX

:: DOWNLOAD

TreeEdit

:: MORE INFORMATION

TreeStat 1.2 – Calculate Summary Statistics of a set of Trees

TreeStat 1.2

:: DESCRIPTION

TreeStat is an application that can process a set of trees in a PHYLIP or NEXUS format tree file and calculate a number of summary statistics for each. These are saved in a tab-delimited file for analysis in Tracer or statistics packages.

::DEVELOPER

Andrew Rambaut Group

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOS
Java

:: DOWNLOAD

TreeStat

:: MORE INFORMATION