JCVI: Research / Projects / Cloud BioLinux / Included Software
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Cloud BioLinux

Included Open Source Software Packages

The following open source packages are included in the JCVI Cloud Bio-Linux image.

Package nameVersionDescription
Celera Assembler3.5Celera Assembler can reconstruct long sequences of genomic DNA given the fragmentary data produced by whole-genome shotgun sequencing.

Included NEBC Software Packages

The following NEBC packages are included in the JCVI Cloud Bio-Linux image.

Package nameVersionDescription
act8.0-0ACT (Artemis Comparison Tool) is a DNA sequence comparison viewer based on Artemis
ape2.2-1-1APE (Analyses of Phylogenetics and Evolution) is a package written in R.
arb071207-8Graphical sequence and data analysis tools.
artemis11.0-2Artemis is a free genome viewer and annotation tool
assembly-conversion-tools0.01-7Conversion tools for handling 454 assemblies.
backups0.1-3Bio-Linux 5.0 backup utilities.
base-directories1.0-26Essential Bio-Linux configuration files.
big-blast1.0.3-2The big-blast script for annotation of long sequences
biojava1.6-1Open-source Java framework for processing biological data.
blast+2.2.19-1Blast+ contains new builds of the popular blast family of programs from the NCBI.
blast2.20-0Rapid searching of nucleotide and protein databases.
bldp-files1.1-44Documentation for bioinformatics software on Bio-Linux.
blixem3.0-5Interactive browser for viewing pairwise Blast results.
cap320020829-2 A base calling system.
cd-hit2007-0131-3cd-hit is a suite of programs designed to quickly group sequences.
clcworkbench2.00-3CLC Free Workbench is a graphical interface allowing the user to carry out many basic bioinformatics tasks.
clustal1.83-3An integrated environment for multiple sequence and profile alignments.
coalesce1.5b-2Population estimate modelling.
das-prep0.1-2Sets up dependencies necessary for running the DAS Proserver on Bio-Linux
dendroscope1.4.0-2Dendroscope is an interactive viewer for large phylogenetic trees.
documentation1.0-14Centralised documentation folder for bioinformatics software on Bio-Linux
dotter3.1-4Dotter is a graphical dotplot program for detailed comparison of two sequences.
dotur1.53-2Dotur assigns sequences to operational taxonomic units (OTUs) using information in a distance matrix.
dust0.1-1Dust - repetitive sequence masker
eclipse3.0-4Universal development tool.
emboss-kmenus0.98-2Gnome and KDE menu entries and wrapper scripts for EMBOSS.
emboss6.0.1-6Emboss contains an extensive set of tools for bioinformatics and biological database management.
envbase-for-pedro2.0-10Settings and template for Pedro.
estscan2.0-5Program for detecting coding regions of DNA sequences.
exchanger0.2-4Exchanger lets you store, annotate and share files via an omixed server.
fasta35t4d8-1Collection of programs for searching DNA and protein databases.
fastDNAml1.2.2-4fastDNAml is a program for estimating maximum likelihood phylogenetic trees from nucleotide sequences.
fluctuate1.4-2Population modelling software.
forester1.92-7ATV (A Tree Viewer) is a Java tool for the visualization of annotated phylogenetic trees.
genespring-27.3-2Transcriptomics data analysis tool from Agilent Technologies.
genquery2.2.3-1GenQuery is a set of Perl libraries for managing SQL query templates and making web-based query forms.
glimmer2.13-4Glimmer is a system for finding genes in microbial DNA.
glimmer33.02-1Glimmer is a system for finding genes in microbial DNA.
grid-certs1.0-1NGS CA root certificates as of November 2007.
grid1.8.1-1Grid middleware bundle comprising of subsection of the vdt suite.
gsrint1.0-2Scripts for use within GeneSpring
handlebar2.2.2-2Database for storing data about barcodes and accessing via a web front-end.
happy1.2-1HAPPY: a software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals
hmmer2.3.2-5HMM methods for searching databases for multiple sequence alignments.
jalview2.40-0Jalview is a Java multiple alignment editor
keyring0.1Public key package for the Bio-Linux package repository
lamarc2.1.3-1Estimates population parameters using Likelihood Analysis using Random Coalescence.
lucy1.19p-5Preparation of raw DNA sequence fragments for sequence assembly.
maxd2.3.0-4maxd is a data warehouse and visualisation environment for genomic expression data.
mcl06-058-4Tools for clustering protein groups in to protein families.
mesquite2.5-2Mesquite is software for evolutionary biology.
migrate2.1.3-2Estimates effective population sizes and past migration rates between n populations.
mira-3rd-party20090621-0Provides useful script for sequence handling.
mira2.9.46-1MIRA: Assembly and editing of nucleotide sequences, including 454 and Solexa support
mountapp1.0-3Mountapp provides a small docked area for mounting filesystems
mrbayes-multi3.1.2-7Multiprocessor version of MrBayes.
mrbayes3.1.2-3MrBayes is a program for the Bayesian estimation of phylogeny.
msatfinder2.0.9Microsatellite Finder
mspcrunch2.5-5MSPcrunch is a BLAST post-processing filter.
mummer3.20-1MUMmer is a system for rapidly aligning entire genomes.
muscle1.00-2A bio-linux wrapper for the muscle package maintained by Steffan Moeller.
mview1.49-2Multiple alignment viewer for sequence database search results.
netblast20071010-1Sequence similarity searching program.
njplot2.2-1Phylogenetic tree drawing program.
nrdb39847.0nrdb can be used to generate quasi-nonredundant protein and nucleotide sequence databases.
ocount0.5-0Ocount - oligonucleotide frequency counter.
oligoarray2.1-7Computation of gene-specific oligonucleotides for genome-scale microarray construction.
oligoarrayaux2.1-2OligoArrayAux 2.1 is free software that is required for the OligoArray2.1 software.
omegamap0.5-1OmegaMap is a program for detecting natural selection and recombination in DNA or RNA sequences.
paml4.0-1Phylogenetic analysis tool for DNA and protein sequences using maximum likelihood.
partigene3.05-3Cluster and anotation tool for sequence data.
pedro1.8-14Data entry tool.
peptidemapper0.1-3A simple peptide mapping tool.
pfaat1.0.034-3Sequence alignment editor designed for protein family analysis.
pftools2.3.4-5Prosite format tools.
phylip3.68-3Tool for inferring phylogenies.
phyml3.0-0PhyML is a phylogeny software based on the maximum-likelihood principle.
prank20080820-1Multiple alignment software.
priam2005.07-2Program to generate enzyme-specific profiles for metabolic pathyway prediction.
primer31.1.4-0Primer3 picks primers for PCR reactions.
prot4est2.2-7Translation of error-prone nucleotide sequences producing robust polypeptide predictions
qtlcart1.17f-8Suite of programs to map quantitative traits using a map of molecular markers.
rasmol2. genetics visualisation tool.
rbs-finder1.0-1A program to find Ribosomal binding sites.
readseq2.2.27-2Read and reformat biosequences, Java command-line version.
recombine1.41-3Population modelling software.
sampledata20041011-7Sample data for Bio-Linux packages
seaview2.4-2Multiple sequence alignment editor.
sequin8.10-2NCBI tool for submitting sequence data to public databases.
splitstree4.0-4Analysis and visualisation tool for distance data from biological sequences.
squint1.02-1Squint is a java-based multiple alignment program and editor
staden2006.1.7.0+1.11.6-2A suite of tools for sequence analysis.
stars1.2a-9STARS is an alternative interface to Staden.
t-coffee6.30-1T-Coffee is a multiple sequence alignment package.
taverna1.70-4Workflow tool that make use of web services.
taxinspector1.0b3-6TaxInspector is a browser for entries in the NCBI taxonomy database.
tetra1.0b3TETRA - tetranucleotide frequency calculator with GUI.
themes-v51.1Graphics, icons, KDE splash screen and a GDM theme for Bio-Linux 5.
themes1.3Graphics, icons, KDE splash screen and a GDM theme for Bio-Linux.
trace2dbest3.14-1Processes trace files into dbEST submissions
transterm-hp2.06-1Transterm finds rho-independent transcription terminators in bacterial genomes.
transterm2.04-beta-0Oligonucleotide frequency counter (ocount).
tree-puzzle5.2-5Pylogenetic tree reconstruction from molecular sequence.
treeview0.5.1-2TreeView is a simple program for displaying phylogenies.
trnascan1.23-3tRNAscan-SE searches for tRNA genes in genomic sequences.
usb-maker0.4-2Script to generate Bio-Linux live memory sticks.
wise22.1.20-4Tool for comparison of biopolymers, DNA, and protein sequence.
yamap1.0.4-2Yet Another Microbial Annotation Pipeline.