Tag: toolbox

FaBox 1.61 – Online FASTA Sequences Toolbox

FaBox 1.61

:: DESCRIPTION

FaBox is a collection of simple and intuitive web services that enable biologists and medical researchers to quickly perform typical task with sequence data. The services makes it easy to extract, edit, and replace sequence headers and join or divide data sets based on header information. Other services include collapsing a set of sequences into haplotypes and automated formatting of input files for a number of population genetics programs, such as ARLEQUIN , TCS and MRBAYES . The toolbox is expected to grow on the basis of requests for particular services and converters in the future.

::DEVELOPER

Palle Villesen Fredsted

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • WebServer
  • PHP

:: DOWNLOAD

 FaBox

:: MORE INFORMATION

Citation

Villesen, P (2007),
FaBox: an online toolbox for fasta sequences,
Molecular Ecology Notes 7 (6), 965-968. doi:10.1111/j.1471-8286.2007.01821.x

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.

Biobox – Toolbox for Biomolecular Modelling

Biobox

:: DESCRIPTION

Biobox is a Python-based toolbox facilitating the implementation of biomolecular modelling methods.

::DEVELOPER

Degiacomi Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

Biobox

:: MORE INFORMATION

Citation:

Rudden LSP, Musson SC, Benesch JLP, Degiacomi MT.
Biobox: a toolbox for biomolecular modelling.
Bioinformatics. 2021 Nov 15:btab785. doi: 10.1093/bioinformatics/btab785. Epub ahead of print. PMID: 34791029.

maplet 1.1.1 – Metabolomics Analysis PipeLinE Toolbox

maplet 1.1.1

:: DESCRIPTION

maplet is an R package for statistical data analysis with a special focus on metabolomics datasets. It allows users to create self-contained analytical pipelines.

::DEVELOPER

Jan Krumsiek lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

maplet

:: MORE INFORMATION

Citation

Chetnik K, Benedetti E, Gomari DP, Schweickart A, Batra R, Buyukozkan M, Wang Z, Arnold M, Zierer J, Suhre K, Krumsiek J.
maplet: An extensible R toolbox for modular and reproducible metabolomics pipelines.
Bioinformatics. 2021 Oct 25:btab741. doi: 10.1093/bioinformatics/btab741. Epub ahead of print. PMID: 34694386.

BMT – Bioinformatics Mini Toolbox

BMT

:: DESCRIPTION

BMT is combination of seven tools including FastqTrimmer, Gene Prediction, DNA Analysis, Translation, Protein analysis and Pairwise and Multiple alignment.

::DEVELOPER

Muhammad Nasir Iqbal

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

BMT

:: MORE INFORMATION

Citation

Iqbal MN, Rasheed MA, Awais M, Chammam W, Kanwal S, Khan SU, Saddick S, Tlili I.
BMT: Bioinformatics mini toolbox for comprehensive DNA and protein analysis.
Genomics. 2020 Nov;112(6):4561-4566. doi: 10.1016/j.ygeno.2020.08.010. Epub 2020 Aug 10. PMID: 32791200.

Tmod 1.1.1 – Toolbox of Motif Discovery

Tmod 1.1.1

:: DESCRIPTION

Tmod (Toolbox of Motif Discovery) is developed for the users of Windows operating systems, and has an easy-to-use graphical user interface (GUI). Tmod integrates twelve motif discovery programs: AlignACE (Roth et al., 1998), BioProspector (Liu et al., 2001), Consensus (Hertz and Stormo, 1999), MEME (Bailey and Elkan, 1994), MDscan (Liu et al., 2002), MotifSampler(Thijs, et al., 2001; Thijs, et al., 2002), SeSiMCMC (Favorov, et al., 2005), GLAM (Frith, et al., 2004), MotifRegressor(Conlon, et al., 2003), YMF(Sinha and Tompa, 2003), Weeder (Pavesi, et al., 2001; Pavesi, et al., 2004; Pavesi, et al., 2004) and Gibbs Motif Sampler (Liu, et al., 1995; Newberg, et al., 2007; Thompson, et al., 2004; Thompson, et al., 2003; Thompson, et al., 2007). The motif finding algorithms included in Tmod have all been widely cited and proved excellent methods in the research field of motif discovery.

::DEVELOPER

Jun Liu

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Tmod

:: MORE INFORMATION

Citation

Hanchang Sun, Yuan Yuan, Yibo Wu, Hui Liu, Jun S. Liu and Hongwei Xie.
Tmod: Toolbox of Motif Discovery.
Bioinformatics 2009; doi: 10.1093/bioinformatics/btp681.

Rainbow beta 1.2 – Toolbox for Phylogenetic Supertree Construction & Analysis

Rainbow beta 1.2

:: DESCRIPTION

Rainbow is a program that provides a graphic user interface to construct supertrees using different methods. It also provides tools to analyze the quality of the supertrees produced.

::DEVELOPER

Computational Biology Laboratory, Department of Computer Science , Iowa State University

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Rainbow

:: MORE INFORMATION

Citation

D. Chen, O. Eulenstein and D. Fernández-Baca
Rainbow: a toolbox for phylogenetic supertree construction and analysis
Bioinformatics (2004) 20 (16): 2872-2873.

Cyni 1.0.0.beta6 – Cytoscape Network Inference Toolbox

Cyni 1.0.0.beta6

:: DESCRIPTION

Cyni (Cytoscape Network Inference Toolbox) is a new Cytoscape App that puts together several tools that allow infering networks from biological data. Each of the tools can be used independently or together to perform several tasks.

::DEVELOPER

Systems Biology Lab, Institut Pasteur, Paris

:: SCREENSHOTS

Cyni

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java
  • Cytoscape

:: DOWNLOAD

 Cyni

:: MORE INFORMATION

Citation

The Cyni framework for network inference in Cytoscape.
Guitart-Pla O, Kustagi M, Rügheimer F, Califano A, Schwikowski B.
Bioinformatics. 2014 Dec 18. pii: btu812.