repDNA 1.1.4 – Generate various modes of Feature Vectors for DNA Sequences

repDNA 1.1.4

:: DESCRIPTION

repDNA (Representations of DNAs) is a Python package for generating the widely used features reflecting the physicochemical properties and sequence-order effects of DNAs and nucleotides.

::DEVELOPER

Liu Lab, Harbin Institute of Technology Shenzhen Graduate School.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

 repDNA 

:: MORE INFORMATION

Citation

repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects.
Liu B, Liu F, Fang L, Wang X, Chou KC.
Bioinformatics. 2014 Dec 10. pii: btu820.

WBSA – Bisulfite Sequencing Data Analysis

WBSA

:: DESCRIPTION

WBSA (Web Service for Bisulfite Sequencing Data Analysis) is a free web service for analysis of Whole-Genome Bisulfite-Sequencing (WGBS) and Genome-wide Reduced Representation Bisulfite Sequencing (RRBS) data.

::DEVELOPER

Beijing Institute of Genomics, Chinese Academy of Sciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2014 Jan 30;9(1):e86707. doi: 10.1371/journal.pone.0086707. eCollection 2014.
WBSA: web service for bisulfite sequencing data analysis.
Liang F, Tang B, Wang Y, Wang J, Yu C, Chen X, Zhu J, Yan J, Zhao W, Li R.

HighSSR 1.1 – Microsatellites Markers de novo design and Prediction

HighSSR 1.1

:: DESCRIPTION

HighSSR is a microsatellite prediction framework for microsatellite genotyping based on high-throughput sequencing.

::DEVELOPER

HighSSR team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HighSSR

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Nov 1;28(21):2797-803. doi: 10.1093/bioinformatics/bts524. Epub 2012 Sep 6.
HighSSR: high-throughput SSR characterization and locus development from next-gen sequencing data.
Churbanov A1, Ryan R, Hasan N, Bailey D, Chen H, Milligan B, Houde P.

ClicO FS v2.0.0 – An interactive Web-based service of Circos

ClicO FS v2.0.0

:: DESCRIPTION

ClicO FS  (Circular Interactive Layout Converter Free Services) is an online web-service based on Circos, which provides a user-friendly, interactive web-based interface with configurable features to generate Circos circular plots.

::DEVELOPER

Codon Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

ClicO FS: An interactive web-based service of Circos.
Cheong WH, Tan YC, Yap SJ, Ng KP.
Bioinformatics. 2015 Jul 29. pii: btv433.

PanGP 1.0.1 – Pan-Genome Profile Analyze Tool

PanGP 1.0.1

:: DESCRIPTION

PanGP is a tool for quickly analyzing bacterial pan-genome profile. It has integrated two kinds of sample algorithm, so that it could calculate the pan-genome profile of a population with dozens of or hundreds of strains at extremely low time-cost. At the same time, a user-friendly graphical interface was designed and the image about pan-genome profile could be drawn by PanGP directly.

::DEVELOPER

Yongbing Zhao 

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ Windows
  • Qt
  • openGL
  • C++ compiler

:: DOWNLOAD

 PanGP

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 1;30(9):1297-9. doi: 10.1093/bioinformatics/btu017. Epub 2014 Jan 13.
PanGP: a tool for quickly analyzing bacterial pan-genome profile.
Zhao Y1, Jia X, Yang J, Ling Y, Zhang Z, Yu J, Wu J, Xiao J.

simLoci 1.0 – Simulate Sequence data on an input Topology

simLoci 1.0

:: DESCRIPTION

The script simLoci.py can be used to simulate sequence data on an input topology under a coalescent model with arguments to allow migration between lineages and to modify population parameters.

::DEVELOPER

Deren Eaton

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Python

:: DOWNLOAD

 simLoci

:: MORE INFORMATION

CAT 1.3 – Composition Analysis Toolkit

CAT 1.3

:: DESCRIPTION

CAT (Composition Analysis Toolkit) is a software package that includes a novel measure of codon usage bias, Codon Deviation Coefficient (CDC). Unlike previous measures, CDC effectively accounts for background nucleotide composition in estimating codon usage bias and utilizes a bootstrap assessment of the statistical significance of codon usage bias.

::DEVELOPER

The National Genomics Data Center (NGDC)

:: SCREENSHOTS

:: REQUIREMENTS

  • WIndows/ Linux / MacOsX

:: DOWNLOAD

 CAT

:: MORE INFORMATION

Citation

Zhang, Z., Li, J., Cui, P., Ding, F., Li, A., Townsend, J.P., and Yu, J. (2011)
Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance
BMC Bioinformatics. 2012 Mar 22;13:43.

BLSSPELLER 1.0 – Exhaustive Comparative Motif Discovery

BLSSPELLER 1.0

:: DESCRIPTION

The BLSSpeller software provides 3 main functionalities to the user: de novo comparative motif discovery, pattern matching (with BLS cutoff) and target prediction.

::DEVELOPER

Dieter De Witte Email: dieter.dewitte@intec.ugent.be

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

BLSSpeller

:: MORE INFORMATION

Citation:

De Witte D, Van De Velde J, Decap D, Van Bel M, Audenaert P, Demeester P, Dhoedt B, Vandepoele K, Fostier J.
BLSSpeller: Exhaustive comparative motif discovery of conserved cis-regulatory elements.
Bioinformatics. 2015 Aug 8. pii: btv466.

NgsRelate v2.0 – Estimating Pairwise Relatedness from NGS data

NgsRelate v2.0

:: DESCRIPTION

NgsRelate can be used to infer relatedness coefficients for pairs of individuals from low coverage Next Generation Sequencing (NGS) data by using genotype likelihoods instead of called genotypes.

::DEVELOPER

NgsRelate team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 NgsRelate

:: MORE INFORMATION

Citation

NgsRelate: a software tool for inferring pairwise relatedness from Next Generation Sequencing data.
Korneliussen TS, Moltke I.
Bioinformatics. 2015 Aug 30. pii: btv509

TANGO 1.2.0 – Taxonomic Assignment in Metagenomics

TANGO 1.2.0

:: DESCRIPTION

TANGO  is a tool for the optimal taxonomic assignment of ambiguous pyrosequencing reads.

::DEVELOPER

G. Valiente

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Perl

:: DOWNLOAD

 TANGO

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Jan 1;30(1):17-23. doi: 10.1093/bioinformatics/btt256. Epub 2013 May 3.
Further steps in TANGO: improved taxonomic assignment in metagenomics.
Alonso-Alemany D1, Barré A, Beretta S, Bonizzoni P, Nikolski M, Valiente G.

BMC Bioinformatics. 2011 Jan 7;12:8. doi: 10.1186/1471-2105-12-8.
Flexible taxonomic assignment of ambiguous sequencing reads.
Clemente JC, Jansson J, Valiente G.