Tag: MATLAB

PGEToolbox 3.0 – Matlab Toolbox for Population Genetics and Evolution

PGEToolbox 3.0

:: DESCRIPTION

PGEToolbox is a Matlab-based software package for analysis of polymorphism and divergence data for population genetics and evolution. It estimates several basic statistics of DNA sequence variation and carries out statistical tests of selective neutrality under the infinite alleles model, such as Tajima’s D test, Fu & Li’s tests and Fay & Wu’s H test. The significance of tests is determined from the distribution of the statistics obtained by coalescent simulation. The toolbox performs McDonald-Kreitman test (and several extensions). PGEToolbox also contains functions for handling SNP (Single Nucleotide Polymorphism) genotype data. PGEToolbox is open-sourced, can be easily extended or tailored for specific tasks, and scaled up for large data sets.

::DEVELOPER

Cai Laborary

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  PGEToolbox

:: MORE INFORMATION

Citation:

Cai JJ (2008)
PGEToolbox: A Matlab toolbox for population genetics and evolution
Journal of Heredity Jul-Aug;99(4):438-40. doi:10.1093/jhered/esm127

MBEToolbox 3.0 – MATLAB Molecular Biology & Evolution Toolbox

MBEToolbox 3.0

:: DESCRIPTION

MBEToolbox is a tool which aimed at filling this gap by offering efficient implementations of the most needed functions in molecular biology and evolution. It can be used to manipulate aligned sequences, calculate evolutionary distances, estimate synonymous and nonsynonymous substitution rates, and infer phylogenetic trees. Moreover, it provides an extensible, functional framework for users with more specialized requirements to explore and analyze aligned nucleotide or protein sequences from an evolutionary perspective. The full functions in the toolbox are accessible through the command-line for seasoned Matlab users. A graphical user interface, that may be especially useful for non-specialist end users, is also provided. MBEToolbox is a useful tool that can aid in the exploration, interpretation and visualization of data in molecular biology and evolution.

::DEVELOPER

Cai Laborary

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 MBEToolbox

:: MORE INFORMATION

Citation:

James J Cai, David K Smith, Xuhua Xia, Kwok-yung Yuen.
MBEToolbox 2.0: An enhanced version of a MATLAB toolbox for Molecular Biology and Evolution
Evolutionary Bioinformatics Online 2006, 2 189-192

SBEToolbox 1.3.3 – MATLAB Systems Biology & Evolution Toolbox

SBEToolbox 1.3.3

:: DESCRIPTION

SBEToolbox (Systems Biology and Evolution Toolbox) is being developed in MATLAB as a menu-driven GUI software to determine various statistics of the biological network. Some of its features include (but not limited to) algorithms to create random networks (small-world, ring lattice etc..), deduce clusters in the network (MCL, mCode, clusterOne), compute various network topology measures etc…

::DEVELOPER

Cai Laborary

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SBEToolbox

:: MORE INFORMATION

Citation

Evol Bioinform Online. 2013 Sep 1;9:355-62. doi: 10.4137/EBO.S12012. eCollection 2013.
SBEToolbox: A Matlab Toolbox for Biological Network Analysis.
Konganti K1, Wang G, Yang E, Cai JJ.

KEGGParser 20140324 – Parsing and Editing KEGG Pathway Maps in Matlab

KEGGParser 20140324

:: DESCRIPTION

KEGGParser is a MATLAB based tool for KEGG pathway parsing, semiautomatic fixing, editing, visualization and analysis in MATLAB environment.

::DEVELOPER

 Arsen Arakelyan

:: SCREENSHOTS

KEGGParser

::REQUIREMENTS

  • Linux/ Windows/MacOsX
  • MatLab

:: DOWNLOAD

 KEGGParser

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Feb 15;29(4):518-9. doi: 10.1093/bioinformatics/bts730. Epub 2013 Jan 3.
KEGGParser: parsing and editing KEGG pathway maps in Matlab.
Arakelyan A, Nersisyan L.

Systems Biology Toolbox for MATLAB 1.8

Systems Biology Toolbox for MATLAB 1.8

:: DESCRIPTION

The Systems Biology Toolbox for MATLAB (sbtoolbox) offers systems biologists an open and user extensible environment, in which to explore ideas, prototype and share new algorithms, and build applications for the analysis and simulation of biological systems.

::DEVELOPER

sbtoolbox team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • MatLab

:: DOWNLOAD

 sbtoolbox

:: MORE INFORMATION

Citation

H. Schmidt, M. Jirstrand:
Systems Biology Toolbox for MATLAB: A computational platform for research in Systems Biology,
Bioinformatics Advance Access, November 2005, DOI 10.1093/bioinformatics/bti799

irootlab 0.17.8.22 – MATLAB toolbox for Vibrational Spectroscopy

irootlab 0.17.8.22

:: DESCRIPTION

IRootLab is an open-source project dedicated to providing a MATLAB framework for vibrational spectroscopy. The goal of the project is to provide a comprehensive and user-friendly environment for analysis, whilst facilitating development and validation of algorithms for computational biology using vibrational spectroscopy.

::DEVELOPER

irootlab team

:: SCREENSHOTS

irootlab

:: REQUIREMENTS

  • Linux /  MacOsX / Window
  • matlab

:: DOWNLOAD

 irootlab

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Apr 15;29(8):1095-7. doi: 10.1093/bioinformatics/btt084. Epub 2013 Feb 19.
IRootLab: a free and open-source MATLAB toolbox for vibrational biospectroscopy data analysis.
Trevisan J, Angelov PP, Scott AD, Carmichael PL, Martin FL.

SIMToolbox 2.12- MATLAB toolbox for Structured Illumination Fluorescence Microscopy

SIMToolbox 2.12

:: DESCRIPTION

SIMToolbox is an open-source, modular set of functions for MATLAB designed for processing data acquired by structured illumination microscopy.

::DEVELOPER

Multimedia Technology Group

:: SCREENSHOTS

SIMToolbox

:: REQUIREMENTS

  • Windows
  • MatLab

:: DOWNLOAD

 SIMToolbox

:: MORE INFORMATION

Citation

SIMToolbox: a MATLAB toolbox for structured illumination fluorescence microscopy.
Křížek P, Lukeš T, Ovesný M, Fliegel K, Hagen GM.
Bioinformatics. 2015 Oct 6. pii: btv576.

Convert2Sbml / Convert2Matlab – Convert Metabolic Network Source files into SBML / MATLAB files

Convert2Sbml / Convert2Matlab

:: DESCRIPTION

Convert2Sbml / Convert2Matlab is the Java tool to convert various metabolic network source files into SBML / MATLAB files.

::DEVELOPER

CSB – Computational Systems Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

Convert2Sbml / Convert2Matlab

:: MORE INFORMATION

GridMos 1.0 – Mosaicing tool (in MATLAB) to Improve Cell Counting

GridMos 1.0

:: DESCRIPTION

GridMos is an open-source software tool conceived to build an image mosaic of a hemocytometer’s grid.

::DEVELOPER

GridMos team

:: SCREENSHOTS

GridMos

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • MatLab

:: DOWNLOAD

 GridMos

:: MORE INFORMATION

Citation

Improving reliability of live/dead cell counting through automated image mosaicing.
Piccinini F, Tesei A, Paganelli G, Zoli W, Bevilacqua A.
Comput Methods Programs Biomed. 2014 Dec;117(3):448-63. doi: 10.1016/j.cmpb.2014.09.004

MOCCASIN 1.3.0 – Converting MATLAB ODE models to SBML

MOCCASIN 1.3.0

:: DESCRIPTION

MOCCASIN (Model ODE Converter for Creating Automated SBML INteroperability) is designed to convert certain basic forms of ODE simulation models written in MATLAB or Octave and translate them into SBML format

::DEVELOPER

MOCCASIN team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • MatLab

:: DOWNLOAD

 MOCCASIN

:: MORE INFORMATION

Citation

MOCCASIN: converting MATLAB ODE models to SBML.
Gómez HF, Hucka M, Keating SM, Nudelman G, Iber D, Sealfon SC.
Bioinformatics. 2016 Feb 9. pii: btw056.