PhyNav 1.0 – Reconstruct Evolutionary Relationship among Contemporary Species based on Genetic data

PhyNav 1.0

:: DESCRIPTION

PhyNav (Phylogenetic Navigator)is a tree sampling method to reconstruct phylogenetic trees from really large datasets (DNA and protein). The method combines different methods to sample good trees.

::DEVELOPER

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

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

PhyNav

:: MORE INFORMATION

Citation:

Le Sy Vinh, Heiko A. Schmidt and Arndt von Haeseler,
PhyNav: A novel approach to reconstruct large phylogenies,
proceedings of GfKl conference, 2004.

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.

STC 1.2 – Reconstruct Large Phylogenies

STC 1.2

:: DESCRIPTION

STC (shortest triplet clustering algorithm) is a software to reconstruct phylogenies. The main idea is the introduction of a natural definition of so-called k-representative sets. Based on k-representative sets, shortest triplets are reconstructed and serve as building blocks for the STC algorithm to agglomerate sequences for tree reconstruction in O(n2) time for n sequences.

::DEVELOPER

Center of Integrative Bioinformatics Vienna (CIBIV)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOS

:: DOWNLOAD

STC

:: MORE INFORMATION

Citation

Le Sy Vinh and Arndt von Haeseler,
Shortest Triplet Clustering: Reconstructing Large Phylogenies,
BMC-Bioinformatics.6:92. 2005.

T-REX 4.01 – Reconstruct Phylogenetic Trees and Reticulation Networks

T-REX 4.01

:: DESCRIPTION

T-REX (tree and reticulogram reconstruction) is an application to reconstruct phylogenetic trees and reticulation networks from distance matrices. The application includes a number of tree fitting methods like NJ, UNJ or ADDTREE which have been very popular in phylogenetic analysis. At the same time, the software comprises several new methods of phylogenetic analysis such as: tree reconstruction using weights, tree inference from incomplete distance matrices or modeling a reticulation network for a collection of objects or species. T-REX also allows the user to visualize obtained tree or network structures using Hierarchical, Radial or Axial types of tree drawing and manipulate them interactively.

T-REX Online Version

::DEVELOPER

Vladimir Makarenkov

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOSX

:: DOWNLOAD

T-REX

:: MORE INFORMATION

Citation

Makarenkov, V. 2001.
T-Rex: Reconstructing and visualizing phylogenetic trees and reticulation networks,
Bioinformatics 17, 664-668.