Tag: Analysis

EnzFitter 2 – Curve Fitting & Analysis of Enzyme Kinetics Experiments

EnzFitter 2

:: DESCRIPTION

EnzFitter is a generic curve-fitting package which has custom features designed to make it especially suitable for analysis of enzyme kinetics experiments. For example, initial rate and parameter values can be obtained with their confidence limits for single and twin substrate rate data. Built-in models include Michaelis-Menten with or without substrate inhibition, competitive, uncompetitive and mixed inhibition, ternary complex or ordered bi-bi systems and ping-pong with and without inhibition by substrates. You can easily add other models in conventional algebraic syntax.

::DEVELOPER

Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

EnzFitter

:: MORE INFORMATION

Ordering

 

CalcuSyn 2 – Dose-effect analysis

CalcuSyn 2

:: DESCRIPTION

CalcuSyn is the definitive analyzer of combined drug effects, able automatically to quantify phenomena such as synergism and inhibition. Mixed drug treatment is becoming common in the treatment of cancer, AIDS etc, and CalcuSyn is the most widely used software for establishing efficacy in this field. It performs multiple drug dose-effect calculations using the Median Effect methods described by T-C Chou and P. Talalay (Trends Pharmacol. Sci. 4, 450-454).

::DEVELOPER

Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

CalcuSyn

:: MORE INFORMATION

Ordering

 

PCAGEN 1.2.1 – Perform Principal Component Analysis on Gene Frequency Data

PCAGEN 1.2.1

:: DESCRIPTION

PCAGEN is a computer package for Windows which performs Principal Component Analysis (PCA) on gene frequency data. Graphical ordinations of samples are provided and graphs can be saved. Using randomizations, the program also tests the significance of total inertia as well as individual axes inertia.

::DEVELOPER

Jérôme Goudet.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

PCAGEN

:: MORE INFORMATION

COMPONENT 2.0 – Analysis of Evolutionary Trees

COMPONENT 2.0

:: DESCRIPTION

COMPONENT is a computer program for analysing evolutionary trees and is intended for use in studies of phylogeny, tree shape distribution, gene trees/species trees, host-parasite cospeciation, and biogeography.

::DEVELOPER

Professor Rod Page

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

COMPONENT ; Source Code

:: MORE INFORMATION

For a review of COMPONENT see Joe Slowinski’s review in Cladistics 9: 351-353 (1993).

GDA 1.1 – Analyze Discrete Population Genetic Data

GDA 1.1

:: DESCRIPTION

GDA (Genetic Data Analysis) is a software for computing linkage and hardy-weinberg disequilibrium, some genetic distances, and provides method-of-moments estimators for hierarchical F-statistics.

::DEVELOPER

Paul O. Lewis and Dmitri Zaykin

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

GDA

:: MORE INFORMATION

“Genetic Data Analysis” by Bruce S. Weir (1996, Sinaur Associates)

DNA for Windows 2.51 – DNA Sequence Editing & Analysis Program

DNA for Windows 2.51

:: DESCRIPTION

DNA for Windows is a compact, easy to use DNA analysis program, ideal for small-scale sequencing projects.  It is particularly suited to working with chromatogram files from ABI machines, and is one of the few programs able to edit as well as view these files.  The program has powerful DNA translation and restriction enzyme analysis facilities, and works with external programs to produce multiple alignments and contigs with ease.

::DEVELOPER

David Dixon

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

DNA for Windows

:: MORE INFORMATION

If you find the program useful, don’t forget to register – you will receive the latest version which already has a number of significant improvements over the evaluation version.

VariScan 2.0.3 – Analysis of DNA Sequence Polymorphisms at the Whole Genome-scale

VariScan 2.0.3

:: DESCRIPTION

VariScan is a software package for the analysis of DNA sequence polymorphisms at the whole genome-scale. The software, i) allows estimating a number of population genetic parameters; ii) conducts the analysis by using the sliding window or a wavelet transform-based methods to capture relevant information from DNA polymorphism data; iii) permits the visualization of the results by commonly used genome browsers.

::DEVELOPER

Molecular Evolutionary Genetics Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX/  Linux
  • C++ Complier

:: DOWNLOAD

VariScan

:: MORE INFORMATION

Citation

Hutter, S., Vilella, A, J. and Rozas, J. (2006).
Genome-wide DNA polymorphism analyses using VariScan.
BMC Bioinformatics 7: 409.

DnaSP 5.10.01 – Analysis of Nucleotide Polymorphism from Aligned DNA Sequence Data

DnaSP 5.10.01

:: DESCRIPTION

DnaSP （DNA Sequence Polymorphism） is a software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters.

::DEVELOPER

J. Rozas, P. Librado, J. C. Sánchez-DelBarrio, X. Messeguer and R. Rozas
Molecular Evolutionary Genetics Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

DnaSP

:: MORE INFORMATION

Citation

Librado, P. and Rozas, J. 2009.
DnaSP v5: A software for comprehensive analysis of DNA polymorphism data.
Bioinformatics 25: 1451-1452 | doi: 10.1093/bioinformatics/btp187.

MAPL98 – Linkage Mapping & QTL Analysis

MAPL98

:: DESCRIPTION

MAPL98 is a software for constructing  detailed linkage maps of organisms and analysis of quantitative trait loci(QTLs) and can be run on a personal computer which will be available in an  ordinal laboratory. It provides experimenter freindly computer environment.

::DEVELOPER

Yasuo UKAI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

MAPL98

:: MORE INFORMATION

When you publish a paper including results which were obtained by utilizing Mapl, then please put a short sentence in your paper telling that “Mapl98 was used.” .

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