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Installed tools

Here you can find a list for all the tools and databases installed on the eBioKit

Tool nameTypeAccessVersionDescription
ArtemisToolDownloadable resource-Artemis is a free genome browser and annotation tool that allows visualization of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.
BamtoolsToolCommand-line2.2.3A fast, flexible C++ API & toolkit for reading, writing, and manipulating BAM files.
BEAMToolCommand-line, Galaxy tool2SNP-SNP interaction association mapping based on SNP-block models, infers both SNP association and SNP block structures.
BioLinuxImageDownloadable resource8Bio-Linux is a fully featured, powerful, configurable and easy to maintain bioinformatics workstation. Bio-Linux provides more than 500 bioinformatics programs on an Ubuntu Linux base. There is a graphical menu for bioinformatics programs, as well as easy access to the Bio-Linux bioinformatics documentation system and sample data useful for testing programs.
BioMartDatabaseWeb-based0.7BioMart is a generic data management system which offers a range of advanced query interfaces and administration tools.
BowtieToolCommand-line1.0.1An ultrafast, memory-efficient short read aligner.
Bowtie2ToolCommand-line, Galaxy tool2.2.3Fast and sensitive read aligner.
BWAToolCommand-line, Galaxy tool0.7.9aFast and accurate long-read alignment with Burrows-Wheeler Transform.
ChipsterImageDownloadable resource-Chipster is a user-friendly analysis software for high-throughput data. It contains over 300 analysis tools for next generation sequencing (NGS), microarray, proteomics and sequence data. Users can save and share automatic analysis workflows, and visualize data interactively using a built-in genome browser and many other visualizations.
Clustal OmegaToolCommand-line, Galaxy tool1.2.1Multiple sequence alignment program for proteins.
Clustal 2 W/XToolCommand-line, Galaxy tool2.1Multiple alignment of nucleic acid and protein sequences
Cufflinks, Cuffdiff and CuffmergeToolCommand-line, Galaxy tool2.2.1Assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
DendroscopeToolDownloadable resource3.2.10Dendroscope is an interactive computer software program written in Java for viewing Phylogenetic trees. This program is designed to view trees of all sizes and is very useful for creating figures. Dendroscope can be used for a variety of analyses of molecular data sets but is particularly designed for metagenomics or analyses of uncultured environmental samples.
EMBOSSToolCommand-line, Galaxy tool6.6.0European Molecular Biology Open Software Suite, a free open source software analysis package specially developed for the needs of the molecular biology and bioinformatics user community.
Ensembl bacteriaDatabaseWeb-based22The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online.
Ensembl fungiDatabaseWeb-based22The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online.
Ensembl mammalsDatabaseWeb-based75The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online.
Ensembl metazoaDatabaseWeb-based22The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online.
Ensembl plantDatabaseWeb-based22The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online.
Ensembl protistsDatabaseWeb-based22The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online.
FastQCToolCommand-line, Galaxy tool0.11.2A simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines
FastXToolCommand-line, Galaxy tool0.0.13A set of command line tools for processing of FASTA/FASTQ data files.
FreeBayesToolCommand-line, Galaxy tool0.9.9Bayesian haplotype-based polymorphism discovery and genotyping.
GalaxyToolWeb-based-Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research.
GATK2ToolCommand-line, Galaxy tool3.1.1A software package developed at the Broad Institute to analyze next-generation resequencing data.
GlimmerToolCommand-line, Galaxy tool3.02A system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.
GMAJToolGalaxy tool2.0.1Tool designed for viewing and manipulating Generalized Multiple Alignments.
GMOD in a BoxImageDownloadable resource2.05GMOD in a Box is a GMOD virtual server equipped with a suite of preconfigured GMOD components, including a Chado database, GBrowse2, JBrowse, Tripal, and Apollo or WebApollo. Setting up a GMOD in a Box instance is quick and easy; it even comes with demo data to explore if you do not have your own. If you are investigating GMOD for the first time, GMOD in a Box provides an excellent way to assess GMOD components without having to do any installation; for longer-term uses, the virtual server can be kept running as long as required, and data can easily be moved when new versions of GMOD in a Box are released.
HMMERToolGalaxy tool, Command-line, Downloadable resource3.1b1Profiles protein sequence data using hidden Markov models of a statistical description of a sequence family's consensus.
HYPHYToolCommand-line2.22A flexible and unified platform for carrying out likelihood-based analyses on multiple alignments of molecular sequence data, with the emphasis on studies of rates and patterns of sequence evolution.
JalviewToolWeb-based, Command-line, Downloadable resource-A free program for multiple sequence alignment editing, visualisation and analysis. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation.
LastzToolCommand-line, Galaxy tool1.02A tool for aligning two DNA sequences, and inferring appropriate scoring parameters automatically.
MACSToolCommand-line, Galaxy tool1.4.2Model-based Analysis for ChIP-Seq
MauveToolDownloadable resource2.3.1Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignment provides a basis for research into comparative genomics and the study of evolutionary dynamics. Aligning whole genomes is a fundamentally different problem than aligning short sequences.
MEGANToolDownloadable resource5.5.3MEtaGenome ANalyzer provides tools for optimized analysis of large metagenomic datasets. All the interactive tools you need in one application.
Meme SuiteToolCommand-line, Galaxy tool4.14A collection of tools for the discovery and analysis of sequence motifs.
MrBayesToolGalaxy tool, Downloadable resource3.2.3MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters.
MRSDatabaseWeb-based, Command-line6.0.3A search engine for biological and medical databanks that provides tools to rapidly and reliably download, store, index, and query flat-file lot of databanks.
MUMmerToolDownloadable resource3.23MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.
NCBI BlastToolWeb-based, Command-line2.2.26Basic Local Alignment Search Tool is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.
NCBI Blast+ToolWeb-based, Command-line2.2.29+Enhanced version of the Basic Local Alignment Search Tool algorithm.
NeATToolWeb-based, Command-line-Network Analysis Tools (NeAT), a set of tools performing basic operations on networks and clusters. The web interface gives a convenient and intuitive access to the tools, and allows you to bring your data sets through some typical analysis work flows in order to extract the best of it.
PassToolCommand-line, Galaxy tool2Peak calling in ChIP data based on Poisson de-clumping, controls FWER and FDR. This tool allows the user to provide a prior distribution where they believe the protein may bind to, so that the power can be improved (while still maintain a desired FDR or FWER)
PeakSplitterToolCommand-line1Subdivision of ChIP-seq/ChIP-chip regions into discrete signal peaks
PerMToolGalaxy tool, Command-line0.2.6A software package which was designed to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms.
PerlToolCommand-line5.16.2A high-level, general-purpose, interpreted, dynamic programming language.
PLINKToolWeb-based, Downloadable resource1.07A free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
ProdigalToolDownloadable resource2.6.1Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.
PythonToolCommand-line2.7.6A high-level, general-purpose, interpreted, dynamic programming language.
RToolCommand-line3.1.1A programming language and software environment for statistical computing and graphics.
RNAmmerToolDownloadable resource1.2RNAmmer predicts genes for ribosomal RNA (rRNA) in full genome sequences using hidden Markov models trained on data from the 5S ribosomal RNA database and the European ribosomal RNA database project.
RSATToolWeb-based, Command-line, Downloadable resource-Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities.
SamtoolsToolCommand-line, Galaxy tool0.1.19A set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM (Sequence Alignment/Map), BAM (Binary Alignment/Map) and CRAM formats.
StadenToolDownloadable resource2.0.0b10Staden is a fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
STATegraEMSToolWeb-based0.6r1STATegra EMS is an Experiment Management System (EMS) for omics experiments that supports different types of sequencing-based assays, proteomics and metabolomics data.
The system has been developed to provide research laboratories with an integrated system that offers a simple and effective way for experiment annotation and tracking of analysis pipelines from raw data to ready-to-use measurements, using free, open source software technologies.
TopHatToolCommand-line, Galaxy toolv2.0.12A fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
TrinityToolCommand-line-Trinity assembles transcript sequences from Illumina RNA-Seq data.
tRNAscan-SEToolDownloadable resource-tRNAscan-SE identifies transfer RNA genes in genomic DNA or RNA sequences.
UGENEToolDownloadable resource1.14.1UGENE is free open-source bioinformatics software. It works on a desktop computer with Windows, Mac OS X or Linux.
UGENE helps biologists to analyze various biological data, such as sequences, annotations, multiple alignments, phylogenetic trees, NGS assemblies, and others. The data can be stored both locally (on a personal computer) and on a shared storage (e.g. a lab database).
VCF toolsToolCommand-line, Galaxy tool0.1.12bA suite of functions for use on genetic variation data in the form of VCF and BCF files.
VelvetToolCommand-line, Galaxy tool1.2.10Sequence assembler for very short reads
WebApolloToolWeb-basedv1.0.3WebApollo is a browser-based tool for visualization and editing of sequence annotations. It is designed for distributed community annotation efforts, where numerous people may be working on the same sequences in geographically different locations; real-time updating keeps all users in sync during the editing process.
WeblogoToolWeb-based, Command-linev3.3WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment.
wEMBOSSToolWeb-basedv2.2.1wEMBOSS is a web interface to the popular EMBOSS software package for biological sequence analysis.
WikipediaDatabaseWeb-based-Wikipedia is a multilingual, web-based, free-content encyclopedia project supported by the Wikimedia Foundation and based on a model of openly editable content.