Tag: Calculate

Breakpoint Calculator 0.2.1 – Calculate Breakpoint Counts for each pair and triplet of Genomes

Breakpoint Calculator 0.2.1

:: DESCRIPTION

Breakpoint Calculator calculates pairwise and three-way hidden breakpoint counts for each pair and triplet of genomes.The breakpoint calculator constructs a weighted graph from the adjacencies of the genomes in the alignment and computes a maximum weight perfect matching.

::DEVELOPER

Birte Kehr., Knut Reinert, and Aaron Darling

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

  Breakpoint Calculator

:: MORE INFORMATION

Citation

Birte Kehr, Knut Reinert, Aaron Darling
Hidden breakpoints in genome alignments
WABI 2012

GAAS 0.17 – Calculate Accurate Community Composition and Average Genome Size

GAAS 0.17

:: DESCRIPTION

GAAS (Genome relative Abundance and Average Size) is a bioinformatic tool to calculate accurate community composition and average genome size in metagenomes by using BLAST, advanced parsing of hits and correction of genome length bias.

::DEVELOPER

Florent E. Angly (florent.angly@gmail.com)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GAAS

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2009 Dec;5(12):e1000593. Epub 2009 Dec 11.
The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes.
Angly FE , et al.

TAP 1.8 – Calculate TAP and TAP-k to Evaluate Bioinformatics Retrieval Methods

TAP 1.8

:: DESCRIPTION

TAP calculates the TAP and TAP-k to evaluate bioinformatics retrieval methods.

::DEVELOPER

Statistical Computational Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • Perl

:: DOWNLOAD

  TAP

:: MORE INFORMATION

Citation

H.D. Carroll, M.G. Kann, S.L. Sheetlin, and J.L. Spouge
“Threshold Average Precision (TAP-k): a Measure of Retrieval Efficacy Designed for Bioinformatics”
(2010) Bioinformatics 26 : 1708-1713

PCI 1.0 – Calculate Barcode Gap Probability of Correct Identification of Species.

PCI 1.0

:: DESCRIPTION

PCI calculates the barcode gap probability of correct identification (PCI) of species.

::DEVELOPER

Statistical Computational Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • Perl

:: DOWNLOAD

 PCI

:: MORE INFORMATION

Citation

N. Suwannasai, M.P. Martín, C. Phosri, P. Sihanonth, A.J.S. Whalley and J.L. Spouge
“Fungi in Thailand: A Case Study of the Efficacy of an ITS Barcode for Automatically Identifying Species within the Annulohypoxylon and Hypoxylon Genera”
PLoS One. 2013;8(2):e54529.

REGENT 1.0.5 – Calculate Risks Conferred by Genetic Factors and Multi-level Environmental Factors

REGENT 1.0.5

:: DESCRIPTION

REGENT (Risk Estimation for Genetic and Environmental Traits) is an R package to calculate risks conferred by genetic factors and multi-level environmental factors.  This is performed at a population level, with the option to also analyse individual-level data.  REGENT incorporates variability in risk factors to calculate confidence intervals for risk estimates and to classify the population into different categories of risk based on significant differences from the baseline average member of the population.

::DEVELOPER

Professor Cathryn Lewis’ Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 REGENT

:: MORE INFORMATION

Citation

Eur J Hum Genet. 2013 Jan;21(1):109-11. doi: 10.1038/ejhg.2012.107. Epub 2012 Jun 6.
REGENT: a risk assessment and classification algorithm for genetic and environmental factors.
Crouch DJ, Goddard GH, Lewis CM.

kcoeff – Calculate Genetic Relatedness from SNP data

kcoeff

:: DESCRIPTION

kcoeff is a program that accepts SNP genotype data as input and calculates K0, K1, and K2.

::DEVELOPER

the Pevsner Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 kcoeff

:: MORE INFORMATION

Citation

Stevens EL, Heckenberg G, Roberson EDO, Baugher JD, Downey TJ, et al. (2011)
Inference of Relationships in Population Data Using Identity-by-Descent and Identity-by-State.
PLoS Genet 7(9): e1002287. doi:10.1371/journal.pgen.1002287

MetAl 1.1 – Calculate Metric Distances between Alternative Alignments of the same Sequences

MetAl 1.1

:: DESCRIPTION

MetAl is a command-line utilty for calculating metric distances between alternative alignments of the same sequences.

::DEVELOPER

Whelan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  MetAl

:: MORE INFORMATION

Citation

Blackburne BP, Whelan, S. (2012).
Measuring the distance between multiple sequence alignments.
Bioinformatics, 28, 495-502.

Convergence – Calculate Divergence and Convergence using Modifications of the Codeml program

Convergence

:: DESCRIPTION

Convergence  is a software for calculation of posterior convergent and divergent substitution probabilities and their expected counts, using posterior integration and amino-acid substitution models: “codeML-ancestral”

::DEVELOPER

Pollock Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

:: MORE INFORMATION

Citation

Evidence for an ancient adaptive episode of convergent molecular evolution.
Castoe TA, de Koning AP, Kim HM, Gu W, Noonan BP, Naylor G, Jiang ZJ, Parkinson CL, Pollock DD.
Proc Natl Acad Sci U S A. 2009 Jun 2;106(22):8986-91. Epub 2009 Apr 28.

jlogP 2.3 – Calculates Hydrophobicity & Molecular Formula of Molecules

jlogP 2.3

:: DESCRIPTION

jlogP is a java applet to calculate the hydrophobicity and molecular formula of molecules drawn by the user.

::DEVELOPER

Brian White

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

jlogP

:: MORE INFORMATION

CLENCH 2.0 – Calculate Cluster Enrichment using the Gene Ontology

CLENCH 2.0

:: DESCRIPTION

CLENCH is a program for calculating cluster enrichment using the Gene Ontology. Analysis of microarray data most often produces lists of genes with similar expression patterns, which are then subdivided into functional categories for biological interpretation. Such functional categorization is most commonly accomplished using Gene Ontology (GO) categories. Although there are several programs that identify and analyze functional categories for human, mouse and yeast genes none, of them accept Arabidopsis thaliana data. In order to address this need for A. thaliana community, we have developed a program that retrieves GO annotations for A. thaliana genes and performs functional category analysis for lists of genes selected by the user.

::DEVELOPER

Nigam Shah

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • perl

:: DOWNLOAD

  CLENCH

:: MORE INFORMATION

Citation

Bioinformatics. 2004 May 1;20(7):1196-7. Epub 2004 Feb 5.
CLENCH: a program for calculating Cluster ENriCHment using the Gene Ontology.
Shah NH, Fedoroff NV.