HomologMiner 1.00 – Find Homologous Genomic Groups in Whole Genomes

HomologMiner 1.00

:: DESCRIPTION

HomologMiner is a software to identify homologous groups applicable to genome sequences that have been properly marked for low-complexity repeats and annotated interspersed repeats.

::DEVELOPER

Minmei Hou

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 HomologMiner

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Apr 15;23(8):917-25. Epub 2007 Feb 18.
HomologMiner: looking for homologous genomic groups in whole genomes.
Hou M, Berman P, Hsu CH, Harris RS.

BSMAP 2.90 – Whole Genome Bisulfite Sequence MAPping program

BSMAP 2.90

:: DESCRIPTION

BSMAP(Bisulfite Sequence Mapping Program)is a short reads mapping software for bisulfite sequencing reads. Bisulfite treatment converts unmethylated Cytosines into Uracils (sequenced as Thymine) and leave methylated Cytosines unchanged, hence provides a way to study DNA cytosine methylation at single nucleotide resolution. BSMAP aligns the Ts in the reads to both Cs and Ts in the reference.

::DEVELOPER

Li Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

BSMAP

:: MORE INFORMATION

Citation:

BSMAP: whole genome bisulfite sequence MAPping program.
Xi Y, Li W.
BMC Bioinformatics. 2009 Jul 27;10:232. doi: 10.1186/1471-2105-10-232.

Bioinformatics. 2012 Feb 1;28(3):430-2. doi: 10.1093/bioinformatics/btr668. Epub 2011 Dec 6.
RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing.
Xi Y, Bock C, Müller F, Sun D, Meissner A, Li W.

DiscoverY – Y-contig Identification from Whole Genome Assemblies

DiscoverY

:: DESCRIPTION

DiscoverY is a tool to shortlist Y-specific contigs from an assembly of male whole genome sequencing data, based on exact k-mer matches with a female.

::DEVELOPER

Medvedev Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

DiscoverY

:: MORE INFORMATION

Citation:

Rangavittal, S., Stopa, N., Tomaszkiewicz, M. et al.
DiscoverY: A Classifier for Identifying Y Chromosome Sequences in Male Assemblies
BMC Genomics (2019) 20: 641.

PLINK 1.90 b – Whole Genome Association Analysis Toolset

PLINK 1.90 b

:: DESCRIPTION

PLINK is a comprehensive toolset for statistical analysis in whole-genome association studies, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

::DEVELOPER

Purcell Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows

:: DOWNLOAD

PLINK

:: MORE INFORMATION

Citation

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC (2007)
PLINK: a toolset for whole-genome association and population-based linkage analysis.
American Journal of Human Genetics, 81.

UnderlyingApproach – Alignment-Free Phylogeny of Whole Genomes using Underlying Subwords

UnderlyingApproach

:: DESCRIPTION

The Underlying Approach (UA) builds a scoring function based on this set of patterns, called underlying. This set is by construction linear in the size of input, without overlaps, and can be efficiently constructed. Results show the validity of our method in the reconstruction of phylogenetic trees, where the Underlying Approach outperforms the current state of the art methods. Moreover, the accuracy of UA is achieved with a very small number of subwords, which in some cases carry meaningful biological information.

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 UnderlyingApproach

:: MORE INFORMATION

Citation

Algorithms Mol Biol. 2012 Dec 6;7(1):34. doi: 10.1186/1748-7188-7-34.
Alignment-free phylogeny of whole genomes using underlying subwords.
Comin M, Verzotto D.

wgd – Whole Genome Duplication analysis in Python

wgd

:: DESCRIPTION

wgd is a Python package and command line interface (CLI) for the analysis of whole genome duplications (WGDs). wgd implements methods for constructing Ks distributions starting from a CDS fasta file, tools for intra-genomic synteny analysis and methods for modeling and visualizing Ks distributions.

::DEVELOPER

Van de Peer Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Python

:: DOWNLOAD

wgd

:: MORE INFORMATION

Citation:

Zwaenepoel, A., and Van de Peer, Y.
wgd – simple command line tools for the analysis of ancient whole genome duplications.
Bioinformatics., bty915, https://doi.org/10.1093/bioinformatics/bty915

GLAPD – Whole Genome based LAMP Primer Design for a set of Target Genome

GLAPD

:: DESCRIPTION

GLAPD can design LAMPP(Loop-mediated isothermal amplification) primer sets based on a whole genome. It can also design LAMP primers for a set of target genomes. Users can specify a group of background genomes.

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Bowtie
  • CUDA driver

:: DOWNLOAD

GLAPD

:: MORE INFORMATION

MethylExtract 1.9.1 – Methylation Maps and SNV calling from Whole Genome Bisulfite Sequencing Data

MethylExtract 1.9.1

:: DESCRIPTION

MethylExtract is a user friendly tool to generate i) high quality, whole genome methylation maps and ii) to detect sequence variation within the same sample preparation.

::DEVELOPER

The group of computational genomics and bioinformatics at Granada University (Spain)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 MethylExtract

:: MORE INFORMATION

Citation

Version 2. F1000Res. 2013 Oct 15 [revised 2014 Feb 21];2:217. doi: 10.12688/f1000research.2-217.v2. eCollection 2013.
MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data.
Barturen G, Rueda A, Oliver JL, Hackenberg M.

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