Tag: Construction

PathwayExplorer 3.0.2 – Construction of Biological Pathway Diagrams

PathwayExplorer 3.0.2

:: DESCRIPTION

The PathwayExplorer is an easy to use and platform independent interactive Java drawing tool for the construction of biological pathway diagrams in a visual way and the annotation of the components and interactions between them. This novel drawing tool integrates the possibilities of charting elements with different attributes (size, color, labels), drawing connections between elements in distinct characteristics (color, structure, width, arrows), as well as adding links to molecular biology databases, promoter sequences, information on the function of the genes or gene products, and references. The result of the editing process is a PNG (portable network graphics) file for the images and XML (extended markup language) file for the appropriate links. Further it is possible to map expression datasets to the pathways by using gene RefSeq ids. It is also possible to use a SOAP interface to access the pathways online.

::DEVELOPER

Genomics & Bioinformatics Graz, Graz University of Technology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • Oracle / PostgreSQL / MySQL

:: DOWNLOAD

 PathwayExplorer

:: MORE INFORMATION

Citation

Mlecnik B, Scheideler M, Hackl H, Hartler J, Sanchez-Cabo F, Trajanoski Z.
PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways.
Nucleic Acids Res. 33: W633-W637 (2005)

PHLAWD v1 – Phylogenetic Dataset Construction

PHLAWD v1

:: DESCRIPTION

PHLAWD (PHyLogeny Assembly With Databases) is a program written in C++ that constructs datasets from NCBI data (GenBank). This uses the megaphylogeny method to construct extremely large datasets, but is convenient for small ones too.

::DEVELOPER

STEPHEN A. SMITH

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 PHLAWD

:: MORE INFORMATION

Citation

Smith, S. A., J. Beaulieu, A. Stamatakis, and M. J. Donoghue. 2011.
Understanding angiosperm diversification using large and small phylogenies.
American J. of Botany.98: 404-414.

ProfDistS 0.9.9 beta – Construction of Large Phylogenetic Trees

ProfDistS 0.9.9 beta

:: DESCRIPTION

ProfDist is a user-friendly software package using the profile-neighbor-joining method (PNJ) in inferring phylogenies based on profile distances on DNA or RNA sequences. It is a tool for reconstructing and visualizing large phylogenetic trees providing new and standard features with a special focus on time efficency, robustness and accuracy.

::DEVELOPER

Matthias Wolf, Benjamin Ruderisch, Thomas Dandekar, Jörg Schultz, and Tobias Müller Department of Bioinformatics, University Würzburg

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

ProfDistS

:: MORE INFORMATION

Citation

Friedrich J, Dandekar T, Wolf M and Müller T (2005):
ProfDist: A tool for the construction of large phylogenetic trees based on profile distances.
Bioinformatics 21: 2108-2109

TREECON 1.3b – Construction & Drawing of Evolutionary Trees

TREECON 1.3b

:: DESCRIPTION

TREECON is a software package developed primarily for the construction and drawing of phylogenetic trees on the basis of evolutionary distances inferred from nucleic and amino acid sequences. The evolutionary distance is computed for all pairs of organisms (or sequences) and a phylogenetic tree is inferred by considering the relationship between these distance values. In pairwise distance methods, the dissimilarity (fraction of substitutions) is usually converted into evolutionary distance by correcting for multiple mutations. The most frequently used equations to convert dissimilarities into distances are implemented in TREECON. On the basis of these distances, a phylogenetic tree can be inferred. Different algorithms are available to construct a phylogenetic tree and a few of them are implemented in TREECON. Programs for rooting the unrooted evolutionary trees, for drawing the tree on the screen, and for saving the tree are also included, as well as several other tools. Starting from a simple ASCII text file, containing nucleic acid or amino acid sequences with gaps required for mutual alignment, one can produce publishable trees in a user-friendly and straightforward way.

::DEVELOPER

Yves Van de Peer

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

TREECON

:: MORE INFORMATION

Citation

Van de Peer, Y., De Wachter, Y. (1994)
TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment.
Comput. Applic. Biosci. 10, 569-70.