Cloud BioLinux
Included Open Source Software Packages
The following open source packages are included in the JCVI Cloud Bio-Linux image.
| Package name | Version | Description |
| Celera Assembler | 3.5 | Celera 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 name | Version | Description |
| act | 8.0-0 | ACT (Artemis Comparison Tool) is a DNA sequence comparison viewer based on Artemis |
| ape | 2.2-1-1 | APE (Analyses of Phylogenetics and Evolution) is a package written in R. |
| arb | 071207-8 | Graphical sequence and data analysis tools. |
| artemis | 11.0-2 | Artemis is a free genome viewer and annotation tool |
| assembly-conversion-tools | 0.01-7 | Conversion tools for handling 454 assemblies. |
| backups | 0.1-3 | Bio-Linux 5.0 backup utilities. |
| base-directories | 1.0-26 | Essential Bio-Linux configuration files. |
| big-blast | 1.0.3-2 | The big-blast script for annotation of long sequences |
| biojava | 1.6-1 | Open-source Java framework for processing biological data. |
| blast+ | 2.2.19-1 | Blast+ contains new builds of the popular blast family of programs from the NCBI. |
| blast | 2.20-0 | Rapid searching of nucleotide and protein databases. |
| bldp-files | 1.1-44 | Documentation for bioinformatics software on Bio-Linux. |
| blixem | 3.0-5 | Interactive browser for viewing pairwise Blast results. |
| cap3 | 20020829-2 | A base calling system. |
| cd-hit | 2007-0131-3 | cd-hit is a suite of programs designed to quickly group sequences. |
| clcworkbench | 2.00-3 | CLC Free Workbench is a graphical interface allowing the user to carry out many basic bioinformatics tasks. |
| clustal | 1.83-3 | An integrated environment for multiple sequence and profile alignments. |
| coalesce | 1.5b-2 | Population estimate modelling. |
| das-prep | 0.1-2 | Sets up dependencies necessary for running the DAS Proserver on Bio-Linux |
| dendroscope | 1.4.0-2 | Dendroscope is an interactive viewer for large phylogenetic trees. |
| documentation | 1.0-14 | Centralised documentation folder for bioinformatics software on Bio-Linux |
| dotter | 3.1-4 | Dotter is a graphical dotplot program for detailed comparison of two sequences. |
| dotur | 1.53-2 | Dotur assigns sequences to operational taxonomic units (OTUs) using information in a distance matrix. |
| dust | 0.1-1 | Dust - repetitive sequence masker |
| eclipse | 3.0-4 | Universal development tool. |
| emboss-kmenus | 0.98-2 | Gnome and KDE menu entries and wrapper scripts for EMBOSS. |
| emboss | 6.0.1-6 | Emboss contains an extensive set of tools for bioinformatics and biological database management. |
| envbase-for-pedro | 2.0-10 | Settings and template for Pedro. |
| estscan | 2.0-5 | Program for detecting coding regions of DNA sequences. |
| exchanger | 0.2-4 | Exchanger lets you store, annotate and share files via an omixed server. |
| fasta | 35t4d8-1 | Collection of programs for searching DNA and protein databases. |
| fastDNAml | 1.2.2-4 | fastDNAml is a program for estimating maximum likelihood phylogenetic trees from nucleotide sequences. |
| fluctuate | 1.4-2 | Population modelling software. |
| forester | 1.92-7 | ATV (A Tree Viewer) is a Java tool for the visualization of annotated phylogenetic trees. |
| genespring-2 | 7.3-2 | Transcriptomics data analysis tool from Agilent Technologies. |
| genquery | 2.2.3-1 | GenQuery is a set of Perl libraries for managing SQL query templates and making web-based query forms. |
| glimmer | 2.13-4 | Glimmer is a system for finding genes in microbial DNA. |
| glimmer3 | 3.02-1 | Glimmer is a system for finding genes in microbial DNA. |
| grid-certs | 1.0-1 | NGS CA root certificates as of November 2007. |
| grid | 1.8.1-1 | Grid middleware bundle comprising of subsection of the vdt suite. |
| gsrint | 1.0-2 | Scripts for use within GeneSpring |
| handlebar | 2.2.2-2 | Database for storing data about barcodes and accessing via a web front-end. |
| happy | 1.2-1 | HAPPY: a software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals |
| hmmer | 2.3.2-5 | HMM methods for searching databases for multiple sequence alignments. |
| jalview | 2.40-0 | Jalview is a Java multiple alignment editor |
| keyring | 0.1 | Public key package for the Bio-Linux package repository |
| lamarc | 2.1.3-1 | Estimates population parameters using Likelihood Analysis using Random Coalescence. |
| lucy | 1.19p-5 | Preparation of raw DNA sequence fragments for sequence assembly. |
| maxd | 2.3.0-4 | maxd is a data warehouse and visualisation environment for genomic expression data. |
| mcl | 06-058-4 | Tools for clustering protein groups in to protein families. |
| mesquite | 2.5-2 | Mesquite is software for evolutionary biology. |
| migrate | 2.1.3-2 | Estimates effective population sizes and past migration rates between n populations. |
| mira-3rd-party | 20090621-0 | Provides useful script for sequence handling. |
| mira | 2.9.46-1 | MIRA: Assembly and editing of nucleotide sequences, including 454 and Solexa support |
| mountapp | 1.0-3 | Mountapp provides a small docked area for mounting filesystems |
| mrbayes-multi | 3.1.2-7 | Multiprocessor version of MrBayes. |
| mrbayes | 3.1.2-3 | MrBayes is a program for the Bayesian estimation of phylogeny. |
| msatfinder | 2.0.9 | Microsatellite Finder |
| mspcrunch | 2.5-5 | MSPcrunch is a BLAST post-processing filter. |
| mummer | 3.20-1 | MUMmer is a system for rapidly aligning entire genomes. |
| muscle | 1.00-2 | A bio-linux wrapper for the muscle package maintained by Steffan Moeller. |
| mview | 1.49-2 | Multiple alignment viewer for sequence database search results. |
| netblast | 20071010-1 | Sequence similarity searching program. |
| njplot | 2.2-1 | Phylogenetic tree drawing program. |
| nrdb | 39847.0 | nrdb can be used to generate quasi-nonredundant protein and nucleotide sequence databases. |
| ocount | 0.5-0 | Ocount - oligonucleotide frequency counter. |
| oligoarray | 2.1-7 | Computation of gene-specific oligonucleotides for genome-scale microarray construction. |
| oligoarrayaux | 2.1-2 | OligoArrayAux 2.1 is free software that is required for the OligoArray2.1 software. |
| omegamap | 0.5-1 | OmegaMap is a program for detecting natural selection and recombination in DNA or RNA sequences. |
| paml | 4.0-1 | Phylogenetic analysis tool for DNA and protein sequences using maximum likelihood. |
| partigene | 3.05-3 | Cluster and anotation tool for sequence data. |
| pedro | 1.8-14 | Data entry tool. |
| peptidemapper | 0.1-3 | A simple peptide mapping tool. |
| pfaat | 1.0.034-3 | Sequence alignment editor designed for protein family analysis. |
| pftools | 2.3.4-5 | Prosite format tools. |
| phylip | 3.68-3 | Tool for inferring phylogenies. |
| phyml | 3.0-0 | PhyML is a phylogeny software based on the maximum-likelihood principle. |
| prank | 20080820-1 | Multiple alignment software. |
| priam | 2005.07-2 | Program to generate enzyme-specific profiles for metabolic pathyway prediction. |
| primer3 | 1.1.4-0 | Primer3 picks primers for PCR reactions. |
| prot4est | 2.2-7 | Translation of error-prone nucleotide sequences producing robust polypeptide predictions |
| qtlcart | 1.17f-8 | Suite of programs to map quantitative traits using a map of molecular markers. |
| rasmol | 2.7.2.1.1-7 | Molecular genetics visualisation tool. |
| rbs-finder | 1.0-1 | A program to find Ribosomal binding sites. |
| readseq | 2.2.27-2 | Read and reformat biosequences, Java command-line version. |
| recombine | 1.41-3 | Population modelling software. |
| sampledata | 20041011-7 | Sample data for Bio-Linux packages |
| seaview | 2.4-2 | Multiple sequence alignment editor. |
| sequin | 8.10-2 | NCBI tool for submitting sequence data to public databases. |
| splitstree | 4.0-4 | Analysis and visualisation tool for distance data from biological sequences. |
| squint | 1.02-1 | Squint is a java-based multiple alignment program and editor |
| staden | 2006.1.7.0+1.11.6-2 | A suite of tools for sequence analysis. |
| stars | 1.2a-9 | STARS is an alternative interface to Staden. |
| t-coffee | 6.30-1 | T-Coffee is a multiple sequence alignment package. |
| taverna | 1.70-4 | Workflow tool that make use of web services. |
| taxinspector | 1.0b3-6 | TaxInspector is a browser for entries in the NCBI taxonomy database. |
| tetra | 1.0b3 | TETRA - tetranucleotide frequency calculator with GUI. |
| themes-v5 | 1.1 | Graphics, icons, KDE splash screen and a GDM theme for Bio-Linux 5. |
| themes | 1.3 | Graphics, icons, KDE splash screen and a GDM theme for Bio-Linux. |
| trace2dbest | 3.14-1 | Processes trace files into dbEST submissions |
| transterm-hp | 2.06-1 | Transterm finds rho-independent transcription terminators in bacterial genomes. |
| transterm | 2.04-beta-0 | Oligonucleotide frequency counter (ocount). |
| tree-puzzle | 5.2-5 | Pylogenetic tree reconstruction from molecular sequence. |
| treeview | 0.5.1-2 | TreeView is a simple program for displaying phylogenies. |
| trnascan | 1.23-3 | tRNAscan-SE searches for tRNA genes in genomic sequences. |
| usb-maker | 0.4-2 | Script to generate Bio-Linux live memory sticks. |
| wise2 | 2.1.20-4 | Tool for comparison of biopolymers, DNA, and protein sequence. |
| yamap | 1.0.4-2 | Yet Another Microbial Annotation Pipeline. |
Resources
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Email: cloud(AT)jcvi.org