Tag: Topology

SimBioNeT 1.2.16 – Simulator of Biological Network Topology

SimBioNeT 1.2.16

:: DESCRIPTION

SimBioNeT is a biological network topology simulator, in which module structures of different type and size are replicated at different level of network organization and interconnected, so to obtain the desired degree distribution, e.g. scale free, and a clustering coefficient constant with the number of nodes in the network, a typical characteristic of biological networks.

::DEVELOPER

Barbara Di Camillo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • R package

:: DOWNLOAD

  SimBioNeT

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2012 Mar-Apr;9(2). doi: 10.1109/TCBB.2011.116. Epub 2011 Aug 18.
SimBioNeT: A Simulator of Biological Network Topology.
Di Camillo B, Falda M, Toffolo G, Cobelli C.

TreeTest – Testing Phylogenetic Tree Topologies in a Frequentist Framework

TreeTest

:: DESCRIPTION

 TreeTest is a program for testing phylogenetic tree topologies in a frequentist framework.The software makes use of the baseml code (PAML), and implements tests of phylogenetic hypotheses (is the maximum likelihood tree the correct tree?) and significance tests.

::DEVELOPER

The Aris-Brosou lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

  TreeTest

:: MORE INFORMATION

Citaion

Aris-Brosou, S. 2003.
Least and most powerful phylogenetic tests to elucidate the origin of the seed plants in presence of conflicting signals under misspecified models.
Syst. Biol. 52:781-793

TOPS / Tops editor – Topology Of Protein Structure

TOPS / Tops editor

:: DESCRIPTION

TOPS & Tops editor are source code of TPOS dadabase (an enhanced database of protein structural topology).

::DEVELOPER

University of Leeds Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java
  • C Compiler

:: DOWNLOAD

 TOPS / Tops editor

:: MORE INFORMATION

Citation

Ioannis Michalopoulos, Gilleain M. Torrance1, David R. Gilbert1 and David R. Westhead
TOPS: an enhanced database of protein structural topology
Nucl. Acids Res. (2004) 32 (suppl 1): D251-D254.

HMMTOP 2.9 – Predict Transmembrane Helices and Topology of Proteins

HMMTOP 2.9

:: DESCRIPTION

HMMTOP is an automatic server for predicting transmembrane helices and topology of proteins

::DEVELOPER

Gabor E. Tusnády

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 HMMTOP 

:: MORE INFORMATION

Citation:

G.E Tusnády and I. Simon (2001)
The HMMTOP transmembrane topology prediction server
Bioinformatics 17, 849-850

TOADS – TOpologies in Alignments of DNA Sequences

TOADS

:: DESCRIPTION

TOADS (TOpologies in Alignments of DNA Sequences) is a C program to carry out a quick check for recombination in a DNA sequence alignment of 3 or 4 taxa.

::DEVELOPER

Dirk Husmeier 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Matlab

:: DOWNLOAD

 TOADS

:: MORE INFORMATION