Tag: Whole Genome

kSNP 3.1.2 – SNP Discovery and SNP Annotation from Whole Genomes

kSNP 3.1.2

:: DESCRIPTION

kSNP identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs.

::DEVELOPER

Barry G. Hall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

kSNP

:: MORE INFORMATION

Citation

kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome.
Gardner SN, Slezak T, Hall BG.
Bioinformatics. 2015 Sep 1;31(17):2877-8. doi: 10.1093/bioinformatics/btv271.

PLoS One. 2013 Dec 9;8(12):e81760. doi: 10.1371/journal.pone.0081760. eCollection 2013.
When whole-genome alignments just won’t work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes.
Gardner SN, Hall BG.

WhopGenome 0.9.7 – High-speed Access to Whole-genome Variation Data

WhopGenome 0.9.7

:: DESCRIPTION

WhopGenome is a package for R that provides high-speed access to Variant Call Format (VCF) files as e.g. published by the 1000 Genomes Project.. It also reads in alignments from FASTA, Phylip, MAF and other file formats. Provides easy-to-use interfaces to genome annotation from UCSC and Bioconductor and gene ontology data from AmiGO and is capable to read, modify and write PLINK .PED-format pedigree files.

::DEVELOPER

Computational Cell Biology,   Heinrich-Heine-Universität Düsseldorf

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows  / MacOsX
  • R

:: DOWNLOAD

 WhopGenome

:: MORE INFORMATION

Citation

WhopGenome: high-speed access to whole genome variation and sequence data in R.
Wittelsbürger U, Pfeifer B, Lercher MJ.
Bioinformatics. 2015 Feb 1;31(3):413-5. doi: 10.1093/bioinformatics/btu636

MethGo – Analyzing Whole-genome Bisulfite Sequencing data

MethGo

:: DESCRIPTION

MethGo is a simple and effective tool designed for the analysis of data from whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS).

::DEVELOPER

Pao-Yang Chen’s Laboratory 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 MethGo

:: MORE INFORMATION

Citation

MethGo: a comprehensive tool for analyzing whole-genome bisulfite sequencing data.
Liao WW, Yen MR, Ju E, Hsu FM, Lam L, Chen PY.
BMC Genomics. 2015 Dec 9;16 Suppl 12:S11. doi: 10.1186/1471-2164-16-S12-S11.

bsmooth-align 0.8.1 – Analyzing Whole Genome Bisulfite Sequencing (WGBS) data

bsmooth-align

:: DESCRIPTION

bsmooth-align (version 0.8.1). This integrates two different pipelines for aligning WGBS data.

bsseq. This is a R package used for smoothing methylation profiles and identifying DMRs.

bsseqData This is an experiment data package for R, containing an example dataset used in the vignettes (chromosome 21 and 22 from 3 normal colon and 3 colon cancer patients).

::DEVELOPER

RafaLab, Hansen Lab

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioCOnductor

:: DOWNLOAD

 bsmooth-align, bsseq ,bsseqData

:: MORE INFORMATION

Citation

Genome Biol. 2012 Oct 3;13(10):R83.
BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions.
Hansen KD1, Langmead B, Irizarry RA.

WGBSSuite 0.4 – Simulating Whole Genome Bisulphite Sequencing data

WGBSSuite 0.3

:: DESCRIPTION

WGBSSuite is a flexible stochastic simulation tool that generates single-base resolution DNA methylation data genome-wide.

::DEVELOPER

WGBSSuite team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
  • Bsmooth
  • MethylSig

:: DOWNLOAD

  WGBSSuite

:: MORE INFORMATION

Citation

WGBSSuite: Simulating Whole Genome Bisulphite Sequencing data and benchmarking differential DNA methylation analysis tools.
Rackham OJ, Dellaportas P, Petretto E, Bottolo L.
Bioinformatics. 2015 Mar 15. pii: btv114.

SciRoKo 3.4 / SciRoKoCo – Whole Genome Microsatellite Search and Investigation / SSR-search module.

SciRoKo 3.4

:: DESCRIPTION

SciRoKo allows for whole genome microsatellite search and investigation. For example, the whole rice genome may be searched in 55 sec. The integrated microsatellite statistics capabilities makes SciRoKo an powerful tool for comparative genomics.

SciRoKoCo is the command line version for the SciRoKo SSR-search module.

::DEVELOPER

Robert Kofler

:: SCREENSHOTS

SciRoKo

:: REQUIREMENTS

  • Linux / WIndows / MacOsX

:: DOWNLOAD

 SciRoKo

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Jul 1;23(13):1683-5. Epub 2007 Apr 26.
SciRoKo: a new tool for whole genome microsatellite search and investigation.
Kofler R, Schlötterer C, Lelley T.

DualPrime 1.1 – Whole-genome Primer Design software

DualPrime 1.1

:: DESCRIPTION

DualPrime selects PCR primers for construction of gene specific tag (GST) microarrays. It tries to minimize the numbers of primers needed to prime all genes of two genomes (or other two lists of genes).

::DEVELOPER

KTH microarray center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/Windows
  • Perl

:: DOWNLOAD

 DualPrime

:: MORE INFORMATION

Citation:

Bioinformatics. 2005 Feb 1;21(3):325-32. Epub 2004 Aug 27.
Dual-genome primer design for construction of DNA microarrays.
Andersson A, Bernander R, Nilsson P.

3SEQ_2D 20100830 – Detecting Gene Conversion Events in Whole Genomes

3SEQ_2D 20100830

:: DESCRIPTION

3SEQ_2D is a software for detecting gene conversion events in whole genomes.

::DEVELOPER

Miller Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 3SEQ_2D

:: MORE INFORMATION

Citation

J Comput Biol. 2010 Sep;17(9):1281-97. doi: 10.1089/cmb.2010.0103.
An effective method for detecting gene conversion events in whole genomes.
Hsu CH, Zhang Y, Hardison RC; NISC Comparative Sequencing Program, Green ED, Miller W.

Mugsy 1.2.3 – Multiple Whole Genome Alignment tool

Mugsy 1.2.3

:: DESCRIPTION

Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FASTA files and does not require a reference genome.

::DEVELOPER

Samuel V. Angiuoli ,  Dr. Steven Salzberg.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • PErl

:: DOWNLOAD

 Mugsy

:: MORE INFORMATION

Citation

Angiuoli SV and Salzberg SL.
Mugsy: Fast multiple alignment of closely related whole genomes.
Bioinformatics 2011 27(3):334-4

ComPhy – Genome Composite Distance Phylogeny for whole-genome phylogeney inferences

ComPhy

:: DESCRIPTION

ComPhy (Genome Composite Distance Phylogeny)  is a java based tool for whole-genome gene set phylogeney inferences.The software determines a prokaryotic phylogeny by calculating a composite distance based on the comparison of complete gene sets between two genomes. It does not require multiple sequence alignment and is fully automated. The composite distance between two genomes is defined by three components: Gene Dispersion Distance (GDD), Gene Content Distance (GCD), and Genome Breakpoint-based Distance (GBD). GDD quantifies the dispersion of ortholog clusters along the genomic coordinates from one genome to another; GCD measures the level of shared orthologs between two genomes; GBD measures the shared break-points between two genomes. The phylogenetic tree is constructed using a neighbour joining method using Phylip from the distance matrix calculated by the composite distance. ComPhy also provides the performance measure of the generated tree against Bergey’s taxonomy system.

::DEVELOPER

Digital Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 ComPhy

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S5.
ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets.
Lin GN, Cai Z, Lin G, Chakraborty S, Xu D.