CubeX – Calculation of Pairwise Linkage Disequilibrium using Exact Solution

CubeX

:: DESCRIPTION

CubeX calculates haplotype frequencies using the exact solution to the cubic equation rather than an iterative approach.

::DEVELOPER

Tom Gaunt’s group in the MRC IEU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux /Mac OsX / Windows
Python

:: DOWNLOAD

CubeX

:: MORE INFORMATION

Citation:

Gaunt TR, Rodríguez S, Day IN.
Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool ‘CubeX’.
BMC Bioinformatics. 2007 Nov 2;8:428.

NetworkDiversity 1.0.0 – Calculation of beta diversity over Phylogenetic Networks

NetworkDiversity 1.0.0

:: DESCRIPTION

Network Diversity is a software package for calculating beta diversity over split systems, a widely used class of implicit phylogenetic networks.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows /MacOsX
C++ Compiler

:: DOWNLOAD

Network Diversity

:: MORE INFORMATION

Citation

Mol Biol Evol. 2012 Dec;29(12):3947-58. doi: 10.1093/molbev/mss200.
Measuring community similarity with phylogenetic networks.
Parks DH, Beiko RG.

3V 1.3 – Volume Related Calculations

3V 1.3

:: DESCRIPTION

3V (Voss Volume Voxelator) is collection of program for the assessment of volumes in protein files.. These tools include methods for displaying the surface of macromolecules and extracting internal channels.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Neil R. Voss and Mark Gerstein
3V: cavity, channel and cleft volume calculator and extractor‘
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W555–W562.

EDIBLE 20110705 – Make Phylogenetic Information Calculations

EDIBLE 20110705

:: DESCRIPTION

EDIBLE (Experimental Design and Information By Likelihood Exploration.) is a software to perform likelihood calculations based on Markov process models of nucleotide substitution allied with phylogenetic trees, and from these to compute Fisher information measures under different experimental designs. These calculations can be used to answer questions of optimal experimental design in molecular phylogenetics.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows

:: DOWNLOAD

EDIBLE

:: MORE INFORMATION

Citation:

EDIBLE: experimental design and information calculations in phylogenetics.
Massingham T, Goldman N.
Bioinformatics. 2000 Mar;16(3):294-5.

Ktreedist 1.0 – Calculation of the Minimum Branch Length Distance (K tree score) between Phylogenetic Trees

Ktreedist 1.0

:: DESCRIPTION

Ktreedist is a computer program written in Perl that calculates the minimum branch length distance from one phylogenetic tree to another, providing a measure of the difference in topology and relative branch lengths (shape) between two trees

::DEVELOPER

Castresana Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ WIndows/MacOsX
Perl

:: DOWNLOAD

Ktreedist

:: MORE INFORMATION

Citation:

Soria-Carrasco, V., Talavera, G., Igea, J., and Castresana, J. (2007).
The K tree score: quantification of differences in the relative branch length and topology of phylogenetic trees.
Bioinformatics 23, 2954-2956.

NLDMseq – Expression Calculation at both Gene and Isoform levels from RNA-seq data given a Reference Transcriptom

NLDMseq

:: DESCRIPTION

NLDMseq is a bioinformatics tool for expression calculation at both gene and isoform levels from RNA-seq data by considering isoform- and exon-specific read sequencing rate.

::DEVELOPER

Xuejun Liu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX
Python

:: DOWNLOAD

NLDMseq

:: MORE INFORMATION

Citation

Improving RNA-Seq expression estimation by modeling isoform- and exon-specific read sequencing rate.
Liu X, Shi X, Chen C, Zhang L.
BMC Bioinformatics. 2015 Oct 16;16(1):332. doi: 10.1186/s12859-015-0750-6.

CHEMMOL 1.0 – Calculation of Molecular Masses and Chemical Analysis of Compounds

CHEMMOL 1.0

:: DESCRIPTION

CHEMMOL is a freeware program for the calculation of molecular masses and chemical analyses of compounds. It was written with the organic chemist in mind.

::DEVELOPER

Wolf van Heeswijk

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

CHEMMOL

:: MORE INFORMATION

Surface Racer 5.0 – Calculation of Accessible and Molecular Surface Areas and Average Surface Curvature

Surface Racer 5.0

:: DESCRIPTION

Surface Racer calculates exact accessible surface area, molecular surface area and average curvature of molecular surface for macromolecules. The program also analyzes cavities in the protein interior inaccessible to solvent from outside. The output includes the surface parameters for each residue in addition to those for individual atoms.

DEVELOPER

Tsodikov laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX

:: DOWNLOAD

Surface Racer

:: MORE INFORMATION

Citation

Tsodikov, O. V., Record, M. T. Jr. and Sergeev, Y. V. (2002).
A novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature.
J. Comput. Chem., 23, 600-609.

ReadOut – Calculation of Direct and Indirect Readout energy Z-scores for Protein-DNA complexes

ReadOut

:: DESCRIPTION

ReadOut is a server calculates:
(1) The DNA conformational energy and Z-score, and
(2) The direct readout or base-amino acid interaction energy and Z-score for protein-DNA complex structures.

::DEVELOPER

Shandar Ahmad

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Server

:: DOWNLOAD

:: MORE INFORMATION

Citation

ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition.
Ahmad S, Kono H, Araúzo-Bravo MJ, Sarai A.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W124-7.

Helix Packing Pair – Calculation of Helix Packing Angles in Protein Structures

Helix Packing Pair

:: DESCRIPTION

Helix Packing Pair is a program that analyses the geometry and the packing of helicies.

::DEVELOPER

University of Leeds Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX

:: DOWNLOAD

Helix Packing Pair

:: MORE INFORMATION

Citation

Dalton, J.A.R., Michalopoulos, I., and Westhead, D.R. (2003).
“Calculation of helix packing angles in protein structures“.
Bioinformatics 19, 1298-1299