SeqPop – Compute Population Genetics Statistics on Sequence Data

SeqPop

:: DESCRIPTION

SeqPop is a program for computing population genetics statistics on sequence data, including Pn, Theta, Pi(i,j), Kst(*), Fst(*), and their Monte Carlo significance for population subdivision.

::DEVELOPER

the Townsend Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac

:: DOWNLOAD

  SeqPop

:: MORE INFORMATION

Reputer – Compute and Visualize Repeat Structures

Reputer

:: DESCRIPTION

The REPuter program family provides state of the art software solutions to compute and visualize repeats in whole genomes or chromosomes.

::DEVELOPER

Prof. Dr. Stefan Kurtz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac OsX/ Linux

:: DOWNLOAD

 Reputer

:: MORE INFORMATION

Citation

S. Kurtz, J. V. Choudhuri, E. Ohlebusch, C. Schleiermacher, J. Stoye, R. Giegerich:
REPuter: The Manifold Applications of Repeat Analysis on a Genomic Scale.
Nucleic Acids Res., 29(22):4633-4642, 2001.

LocalMove – Compute On-lattice Fits for Biopolymers

LocalMove

:: DESCRIPTION

Local move is a Monte-Carlo approach to the problem of finding best-fitting lattice models for biopolymers. Through a sequence of local moves, e.g. local backbone modifications, it walks through the conformational space, looking for a configuration as close as possible to the input 3D model, while keeping his points on-lattice. After a user-defined condition is triggered, the experiment stops and the currently best model can be retrieved as a PDB file.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W216-22. doi: 10.1093/nar/gkn367. Epub 2008 Jun 13.
LocalMove: computing on-lattice fits for biopolymers.
Ponty Y, Istrate R, Porcelli E, Clote P.

rnapagenumber – Compute Optimal “page number” of an RNA Structure

rnapagenumber

:: DESCRIPTION

rnapagenumber is a web server that computes the optimal “page number” of an RNA structure, input as a PDB file or .ct (mfold connect) file.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

On the page number of RNA secondary structures with pseudoknots.
P. Clote, S. Dobrev, I. Dotu, E. Kranakis. D. Krizanc, J. Urrutia,
J Math Biol. 2012 Dec;65(6-7):1337-57.

RNAbor – Compute Structural Neighbors of an RNA Secondary Structure

RNAbor

:: DESCRIPTION

RNAbor is a web server to compute secondary structural neighbors of a given RNA structure.

::DEVELOPER

Clote Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

E. Freyhult, V. Moulton, P. Clote.
RNAbor: A web server for RNA structural neighbors.
Nucleic Acids Res. 2007 Jul 1;35(Web Server issue):W305-9. Epub 2007 May 25.

DNAmelt r23 – Compute DNA Melting Properties

DNAmelt r23

:: DESCRIPTION

DNAmelt is a Matlab toolbox to compute DNA melting properties using a helicoidal transfer matrix model.

::DEVELOPER

Tom Michoel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Matlab

:: DOWNLOAD

 DNAmelt

:: MORE INFORMATION

Citation:

Phys. Rev. E 73, 011908 (2006) [11 pages]
Helicoidal transfer matrix model for inhomogeneous DNA melting
Tom Michoel and Yves Van de Peer

SuperQ 1.1 – Compute a Phylogenetic Super Network

SuperQ 1.1

:: DESCRIPTION

SuperQ is a program written in Java which computes a phylogenetic super network from a collection of partial phylogenetic trees

::DEVELOPER

The UEA Computational Biology Laboratory at the University of East Anglia (UEA)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • Java

:: DOWNLOAD

 SuperQ

:: MORE INFORMATION

Citation

SuperQ: computing supernetworks from quartets.
Grünewald S, Spillner A, Bastkowski S, Bögershausen A, Moulton V.
IEEE/ACM Trans Comput Biol Bioinform. 2013 Jan-Feb;10(1):151-60. doi: 10.1109/TCBB.2013.8.

nhPhyML – Compute Phylogenetic Trees under non Homogeneous model of DNA sequence Evolution

nhPhyML

:: DESCRIPTION

nhPhyML is a program built to compute phylogenetic trees under the non stationary, non homogeneous model of DNA sequence evolution of Galtier and Gouy (1998).

::DEVELOPER

Bastien Boussau

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Mac OsX

:: DOWNLOAD

  nhPhyML

:: MORE INFORMATION

Citation

Efficient likelihood computations with nonreversible models of evolution.
Boussau B, Gouy M.
Syst Biol. 2006 Oct;55(5):756-68.

Melting 5.2.0 – Compute Nucleic Acid Duplex Melting Temperature

Melting 5.2.0

:: DESCRIPTION

Melting computes, for a nucleic acid duplex, the enthalpy, the entropy and the melting temperature of the helix-coil transitions.Three types of hybridisation are possible: DNA/DNA, DNA/RNA, and RNA/RNA. The program first computes the hybridisation enthalpy and entropy from the elementary parameters of each Crick’s pair by the nearest-neighbor method. Then the melting temperature is computed. The set of thermodynamic parameters can be easely changed, for instance following an experimental breakthrough.

MELTING provides a large set of thermodynamic models to compute the enthalpy and entropy of several structures in the duplex : perfectly matching sequences, single mismatch, tandem mismatch, internal loop, single dangling end, second dangling end, long dangling end (only one to four poly A), single bulge loop, long bulge loop, inosine base (I), hydroxyadenine (A*), azobenzene (cis X_C and trans X_T), locked nucleic acids (Al, Gl, Tl, Cl).

Melting also have online versions:

::DEVELOPER

Computational Systems Neurobiology Group, EBI

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Melting

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 May 16;13:101. doi: 10.1186/1471-2105-13-101.
MELTING, a flexible platform to predict the melting temperatures of nucleic acids.
Dumousseau M1, Rodriguez N, Juty N, Le Novère N.

Personalized PageRank Tool – Compute Personalized PageRank in Protein-protein Interaction Network

Personalized PageRank Tool

:: DESCRIPTION

Personalized PageRank Tool, a Perl script for computing personalized PageRank in protein-protein interaction networks, personalized to some important nodes (e.g., for nodes representing upregulated proteins in proteomics study).

::DEVELOPER

The Uratim Manufacturing Ltd.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Perl

:: DOWNLOAD

 Personalized PageRank Tool

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Feb 1;27(3):405-7. doi: 10.1093/bioinformatics/btq680. Epub 2010 Dec 12.
When the Web meets the cell: using personalized PageRank for analyzing protein interaction networks.
Iván G, Grolmusz V.