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GENOMICS SOFTWARE


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JBrowse logo
JBrowse
The JBrowse Genome Browser
Category: Gene expression, Genomics software

JBrowse is a fast and full-featured scalable genome browser built completely with JavaScript and HTML5. It can run on your desktop, or be embedded in your website (see Bues et al., Genome Biol 17, 66 (2016) doi:10.1186/s13059-016-0924-1).

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JDotter logo
JDotter
Category: DNA alignment, Genomics software

Java Dot Plot Alignments (JDotter) is a platform-independent Java interactive interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences. JDotter runs as a client-server application and can send new sequences to the Dotter program for alignment as well as rapidly access a repository of preprocessed dotplots. JDotter also interfaces with a sequence database or file system to display supplementary feature data. Thus, JDotter greatly s

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MultiMiR Database logo
MultiMiR Database
Category: Genomics software

The R package multiMiR, with web server is a comprehensive collection of predicted and validated miRNA-target interactions and their associations with diseases and drugs. Within this database, investigators can find clues to potential new treatments for various diseases, including cancer. In addition to helping researchers search for relationships between microRNAs and their genetic targets, multiMiR includes drugs that affect these microRNAs and lists associated diseases.The database combines n

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MUMmer logo
MUMmer
From SourceForge
Category: Genomics software

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included wit

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PhageFinder logo
PhageFinder
From SourceForge
Category: Genomics software

Automated Identification of Prophage Regions in Complete Bacterial Genome Sequences

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PHAST logo
PHAST
Category: Genomics software

PHAST is a freely available software package (Cornell University) for comparative and evolutionary genomics. It consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations (see left panel).Like algorithms that assess protein-coding genes, they evaluate variants on the basis of how often the sequence changes between species

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PLINK - Whole genome association analysis toolset logo
PLINK - Whole genome association analysis toolset
Category: Genomics software

PLINK is a popular and computationally efficient software program that offers a comprehensive and well-documented set of automated genome wide association quality control and analysis tools. It is a freely available open source software written in C++, which can be installed on Windows, Mac and Unix machines. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from ra

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ProDeGe. Protocol for Decontamination of Genomes logo
ProDeGe. Protocol for Decontamination of Genomes
Category: Genomics software

ProDeGe is the first fully automated computational protocol for decontamination of genomes. The protocol uses public databases to detect contamination in agenome assembly, then groups contigs into “Clean” or “Contaminant” groups. ProDeGe spits out lists that users can read through to identify contaminants and determine what they mightbe.The standalone software is freely available and can be run on any system that has Perl, R, Prodigal and NCBI Blast installed. (Tennessen et al., ISME J.

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PROVEAN logo
PROVEAN
Category: Genomics software

PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein. PROVEAN is useful for filtering sequence variants to identify nonsynonymous or indel variants that are predicted to be functionally important. The performance of PROVEAN is comparable to popular tools such as SIFT or PolyPhen-2.

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PyClone logo
PyClone
Category: Genomics software

PyClone is a tool for inferring the cellular prevalence of point mutations from deeply sequenced data. It serves as a statistical model for inference of clonal population structures in cancers.The model supports simultaneous analysis of multiple related samples and infers clusters of mutations whose cellular prevalences shift together. Such clusters of mutations can be inferred as mutational genotypes of distinct clonal populations (Roth et al., Nature Meth 11, 396, 2014).

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SMS Sequence Manipulation Suite logo
SMS Sequence Manipulation Suite
Category: Genomics software

The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching, and for program and algorithm testing.

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Sybil logo
Sybil
From SouceForge
Category: Genomics software

Sybil is a web-based software package for comparative genomics. It was developed by the Bioinformatics department at The Institute for Genomic Research (TIGR) and development continues at the J. Craig Venter Institute and Institute for Genome Sciences (IGS) at the University of Maryland Baltimore's School of Medicine. The project has been funded by a variety of sources including: The National Institute of Allergy and Infectious Diseases (NIAID) as part of the NIAID Bioinformatics Resource Center

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VAAST logo
VAAST
Category: Genomics software

VAAST (the Variant Annotation, Analysis and Search Tool) is a probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST can score both coding and non-coding variants, evaluating the cumulative impact of both types of variants simultaneously. VAAST can identify rare variants causing rare genetic diseases, and it can also use both rare and common variants to identify genes responsible for common diseases.

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VarSifter logo
VarSifter
Category: Genomics software

VarSifter is a graphical Java program designed to display, sort, filter, and generally sift variation data from massively parallel sequencing experiments. It is designed to read exome-scale variation data in either a tab-delimited text file with header, or an uncompressed VCF file. The program is written in Java, and should run on any platform with a current Java Virtual Machine.

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