SimPlot 3.5.1 – Sequence Similarity Plotting

SimPlot 3.5.1

:: DESCRIPTION

SimPlot (Similarity Plotting) (as well as bootscanning, quick tree generation, and informative-sites analysis) is a popular tool for recombination analysis.

::DEVELOPER

Stuart Ray, M.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

SimPlot if you cannot make that work, please email me for a download link

:: MORE INFORMATION

Reference to the paper in which author first described SimPlot

Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC.
Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination.
J Virol. 1999 Jan;73(1):152-60.

VisSPA 1.62 – Calculate Frequency of Residues

VisSPA 1.62

:: DESCRIPTION

VisSPA (Visual Signature Pattern Analysis) is a program that accepts an alignment of sequences, interactively analyzes frequencies of residues at each position in groups of sequences and supports the generation of sequence logos. The frequency calculations and program name were initially inspired by VESPA (by Gerry Myers and Bette Korber of Los Alamos National Labs).

::DEVELOPER

Stuart Ray, M.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

VisSPA

:: MORE INFORMATION

Before you download software you need to read disclaimer.

 

VarPlot 1.2 – Similarity Plotting for Alignment of Sequences

VarPlot 1.2

:: DESCRIPTION

VarPlot is a program that accepts an alignment of sequences, and interactively plots sliding-window analyses of genetic distance among sequences or groups of sequences. It is different from SimPlot because in SimPlot, all groups are compared to one query, whereas in VarPlot all groups are compared to one another. Also, VarPlot includes calculation of nonsynonymous and synonymous distance (using the Nei and Gojobori method at present).

::DEVELOPER

Stuart Ray, M.D.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

VarPlot

:: MORE INFORMATION

Before you download software you need to read disclaimer.

 

ReadDepth 0.9.8.4 – Detects Copy Number Aberrations in Deep Sequencing Data

ReadDepth 0.9.8.4

:: DESCRIPTION

The readDepth package for R can detect copy number aberrations by measuring the depth of coverage obtained by massively parallel sequencing of the genome. It achieves higher accuracy than many other packages, and runs much faster by utilizing multi-core architectures to parallelize the processing of these large data sets.

::DEVELOPER

the Bioinformatics Research Laboratory at Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package

:: DOWNLOAD

 ReadDepth

:: MORE INFORMATION

Citation

Miller CA, Hampton O, Coarfa C, Milosavljevic A, 2011
ReadDepth: A Parallel R Package for Detecting Copy Number Alterations from Short Sequencing Reads.
PLoS ONE 6(1): e16327. doi:10.1371/journal.pone.0016327

Batman – Bayesian Tool for Methylation Analysis

Batman

:: DESCRIPTION

Batman is a new tool for analysing DNA methylation data from MeDIP experiments combined with microarray or high-throughput sequencing assays.

::DEVELOPER

Thomas Down

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Batman

:: MORE INFORMATION

Citation:

Thomas A Down et al.
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
Nature Biotechnology 26, 779 – 785 (2008)

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

SeSiMCMC 4.36 – Dig For DNA Motifs Gibbs Sampler

SeSiMCMC 4.36

:: DESCRIPTION

The SeSiMCMC (Sequence Similarities by Markov Chain Monte Carlo) algorithm finds DNA motifs of unknown length and complicated structure, such as direct repeats or palindromes with variable spacers in the middle in a set of unaligned DNA sequences. It uses an improved motif length estimator and careful Bayesian analysis to consider site absence in a sequence.

::DEVELOPER

Alexander Favorov

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WIndows / Linux

:: DOWNLOAD

 SeSiMCMC

:: MORE INFORMATION

Citation:

A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length.
Favorov AV, Gelfand MS, Gerasimova AV, Ravcheev DA, Mironov AA, Makeev VJ.
Bioinformatics. 2005 May 15;21(10):2240-5. Epub 2005 Feb 22.

PDA 20060711 – Pooled DNA Analyzer

PDA 20060711

:: DESCRIPTION

PDA ( Pooled DNA analyzer ) is a powerful tool for analyses of pooled DNA data.

::DEVELOPER

Hsin-Chou Yang and Cathy SJ Fann(Institute of Biomedical Sciences, Academia Sinica, Taiwan)

:: SCREENSHOTS

::REQUIREMENTS

:: DOWNLOAD

 PDA

:: MORE INFORMATION

Citation

Hsin-Chou Yang, Chia-Ching Pan, Chin-Yu Lin and Cathy SJ Fann (2006).
PDA: pooled DNA analyzer.
BMC Bioinformatics, 7: 233.

ChemGenome 2.1 – Gene Prediction Software

ChemGenome 2.1

:: DESCRIPTION

Chemgenome is an ab-intio gene prediction software, which find genes in prokaryotic genomes in all six reading frames. The methodology follows a physico-chemical approach and has been validated on 372 prokaryotic genomes.

::DEVELOPER

Supercomputing Facility for Bioinformatics & Computational Biology, IIT Delhi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  ChemGenome

:: MORE INFORMATION

Citation:

PLoS One. 2010 Aug 26;5(8):e12433.
A phenomenological model for predicting melting temperatures of DNA sequences.
Khandelwal G, Bhyravabhotla J.

MOSGA 2 – Modular Open-Source Genome Annotator

MOSGA 2

:: DESCRIPTION

The MOSGA is a pipeline that easily creates draft genome annotation by a graphical user interface. It combines several specific prediction tools and generates a submission-ready annotation file.

::DEVELOPER

MOSGA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MOSGA

:: MORE INFORMATION

Citation

Martin R, Hackl T, Hattab G, Fischer MG, Heider D.
MOSGA: Modular Open-Source Genome Annotator.
Bioinformatics. 2021 Apr 1;36(22-23):5514-5515. doi: 10.1093/bioinformatics/btaa1003. PMID: 33258916.

Martin R, Dreßler H, Hattab G, Hackl T, Fischer MG, Heider D.
MOSGA 2: Comparative genomics and validation tools.
Comput Struct Biotechnol J. 2021 Sep 28;19:5504-5509. doi: 10.1016/j.csbj.2021.09.024. PMID: 34712396; PMCID: PMC8517542.

 

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