PhyloGeoRef – Java Library for Mapping Phylogenetic Trees and Geographical Information in KML

PhyloGeoRef

:: DESCRIPTION

PhyloGeoRef is a Java library for producing rich kmls containing phylogeneric data that can be rendered in google earth web browser. In biology, phylogenetics is the study of evolutionary relatedness among groups of organisms (e.g. species, populations), which is discovered through molecular sequencing data and morphological data matrices.

::DEVELOPER

Kathryn Iverson (kd.iverson@gmail.com), Apurv Verma (dapurv5@gmail.com)

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Mac OsX / Linux
Java

:: DOWNLOAD

PhyloGeoRef

:: MORE INFORMATION

HyperTree 1.2.2 – Java Phylogenetic Tree Viewer

HyperTree 1.2.2

:: DESCRIPTION

HYPERTREE is a Java phylogenetic tree viewer, with a hyperbolic (‘fish-eye’) view and editing abilities that help in managing very large trees.

::DEVELOPER

kinase.com

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / Mac OsX
Java

:: DOWNLOAD

HyperTree

:: MORE INFORMATION

Citation

Visualizing harge hierarchical clusters in hyperbolic space
J. Bingham, S Sudarsanam
Bioinformatics (2000) 16(7): 660-1

PhyloWidget – View, Edit, and Publish Phylogenetic Trees

PhyloWidget

:: DESCRIPTION

PhyloWidget is a program for viewing, editing, and publishing phylogenetic trees online. It is small, contains a simple yet powerful user interface, and contains many novel features not available in other phylogenetic viewers

::DEVELOPER

Gregory Jordan

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / Mac OsX
Java

:: DOWNLOAD

PhyloWidget

:: MORE INFORMATION

Citation

PhyloWidget: web-based visualizations for the tree of life
Gregory E. Jordan; William H. Piel
Bioinformatics 2008 24: 1641-1642

IQPNNI 3.3.2 – Reconstruct a Phylogenetic Tree based on DNA or Amino Acid Sequence data

IQPNNI 3.3.2

:: DESCRIPTION

IQPNNI (Important Quartet Puzzling and NNI Operation) is introduced to reconstruct a phylogenetic tree based on DNA or amino acid sequence data. Our approach combines various fast algorithms to generate a list of potential candidate trees. The key ingredient is the definition of so-called important quartets (IQs), which allow the computation of an intermediate tree in O(n^2) time for n sequences. The resulting tree is then further optimized by applying the nearest neighbor interchange (NNI) operation. Subsequently a random fraction of the sequences is deleted from the best tree found so far. The deleted sequences are then re-inserted in the smaller tree using the important quartet puzzling (IQP) algorithm.

::DEVELOPER

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

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / MacOsX / Linux

:: DOWNLOAD

IQPNNI

:: MORE INFORMATION

Citation:

Le Sy Vinh and Arndt von Haeseler (2004)
IQPNNI: Moving fast through tree space and stopping in time.
Mol. Biol. Evol., 21(8):1565-1571.

Treecon-Tools 0.1 – Convert Phylogenetic Trees File Formate

Treecon-Tools 0.1

:: DESCRIPTION

Treecon-Toolscontains 3 small programs to convert phylogenetic trees between NH, NHX and Treecon formats.

:: DEVELOPER

Bioinformatics & Systems Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows/MacOsX
TCL/TK

:: DOWNLOAD

Treecon-Tools

:: MORE INFORMATION

UpdownDistance – Tool for comparing phylogenetic trees

UpdownDistance

:: DESCRIPTION

UpdownDistance is a tool for evaluating closeness of tree matches when comparing a query tree P with a data tree D where both P and D are phylogenetic trees. The method computes the Updown distance between P and D

::DEVELOPER

Dr. Jason Tsong-Li Wang

:: REQUIREMENTS

Linux/Windows/MacOsX
Java

:: DOWNLOAD

UpdownDistance

:: MORE INFORMATION

Citation

Jason T. L. Wang, Huiyuan Shan, Dennis Shasha and William H. Piel,
“Fast Structural Search in Phylogenetic Databases,”
Evolutionary Bioinformatics Online, Volume 1, 2005, pp. 37-46.

FamFetch 2.0 – Search for Tree Patterns in Databases of Phylogenetic Trees

FamFetch 2.0

:: DESCRIPTION

FamFetch is the general interface used to query the families databases developed using the HOBACGEN model.

::DEVELOPER

FamFetch Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/MacOsx
Java

:: DOWNLOAD

FamFetch

:: MORE INFORMATION

Citation

Bioinformatics. 2005 Jun 1;21(11):2596-603. Epub 2005 Feb 15.
Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.
Dufayard JF, Duret L, Penel S, Gouy M, Rechenmann F, Perrière G.

newicktree 1.1 – LaTeX package for Drawing of Phylogenetic Trees

newicktree 1.1

:: DESCRIPTION

newicktree is a LaTeX package that allows the easy drawing of Newick (New Hampshire) format phylogenetic trees, by providing a high level interface to the PSTricks package.

::DEVELOPER

DICKS COMPUTATIONAL BIOLOGY GROUP

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Mac OsX
LaTeX

:: DOWNLOAD

newicktree

:: MORE INFORMATION

Citation:

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

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.

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