Important software packages installed and tested on CloudBiolinux

# package (.deb) origin description by cite version pop*)
Debian
Visualize biological macromolecules (...)
284
Debian
Displays and prints phylogenetic trees (...)
126
Debian
Multiple alignment of nucleic acid and protein sequences (...)
96
Debian
Basic Local Alignment Search Tool (...)
64
Debian
the european molecular biology open software suite (...)
45
Debian
Multiple alignment program of protein sequences (...)
37
Debian
Tool to design flanking oligo nucleotides for DNA (...)
35
Debian
Phylogenetic estimation using Maximum Likelihood (...)
32
Debian
Segment-based multiple sequence alignment (...)
31
Debian
Multiple alignment program for amino acid or nucleotide (...)
31
Debian
profile hidden Markov models for protein sequence analysis (...)
30
Debian
Multiple Sequence Alignment (...)
28
Debian
generic tool for pairwise sequence comparison (...)
27
Debian
Efficient sequence alignment of full genomes (...)
26
Debian
PROBabilistic CONSistency-based multiple sequence alignment (...)
25
Debian
next generation suite of BLAST sequence search tools (...)
22
mcl
Debian
Markov Cluster algorithm (...)
17
Debian
package of programs for inferring phylogenies (...)
12
Debian
Bayesian Inference of Phylogeny (...)
8
BioLinux
Multiprocessor version of MrBayes (...)
3.1.2-4
2
BioLinux
NCBI libraries for biology applications (X-based utilities) (...)
1:1bl-2
2
BioLinux
CLC Free Sequence Viewer (...)
6.4-1
1
BioLinux
Collection of programs for searching DNA and protein (...)
36t2d5-0
1
BioLinux
TreeView is a simple program for displaying phylogenies. (...)
1:1bl-0
1
BioLinux
A suite of tools for sequence analysis. (...)
2006.1.7.0+1.11.6-5
1
BioLinux
Multiple sequence alignment editor. (...)
4.2.8-2
1
BioLinux
Population modelling software. (...)
1.4-0
1
BioLinux
Jalview is a Java multiple alignment editor (...)
1:2.6.1-1
1
Debian
integrated bioinformatics toolkit (...)
1
BioLinux
Preparation of raw DNA sequence fragments for sequence (...)
1.20-0
1
BioLinux
maxd is a data warehouse and visualisation environment (...)
2.3.0-5
1
CloudBiolinx
GATK: library for writing efficient analysis tools using (...)
1.6-11-g3b2fab9
BioLinux
Estimates effective population sizes and past migration rates (...)
3.1.2-1
BioLinux
Public key package for the Bio-Linux package repository (...)
4
BioLinux
MSPcrunch is a BLAST post-processing filter. (...)
2.5-0
BioLinux
Multiple alignment viewer for sequence database search results. (...)
1.51-2
BioLinux
HAPPY: a software package for Multipoint QTL Mapping (...)
1.2-1
BioLinux
nrdb can be used to generate quasi-nonredundant protein (...)
2-0
BioLinux
Ocount - oligonucleotide frequency counter. (...)
0.5-0
BioLinux
Computation of gene-specific oligonucleotides for genome-scale microarray construction. (...)
2.1-8
BioLinux
OligoArrayAux 3.7 is free software that is required (...)
3.7-0
BioLinux
OmegaMap is a program for detecting natural selection (...)
0.5-0
BioLinux
Phylogenetic analysis tool for DNA and protein sequences (...)
4.4c-1
BioLinux
Cluster and anotation tool for sequence data. (...)
3.05-8
BioLinux
Sequence alignment editor designed for protein family analysis. (...)
1.0.034-5
BioLinux
Multiple alignment software. (...)
20100318-0
BioLinux
Stop Bio-Linux from upgrading on release of 12.04 (...)
0.2
BioLinux
Translation of error-prone nucleotide sequences producing robust polypeptide (...)
2.2-10
BioLinux
Suite of programs to map quantitative traits using (...)
1.17f-0
BioLinux
A program to find Ribosomal binding sites. (...)
1.0-3
BioLinux
Population modelling software. (...)
1.41-0
BioLinux
Sample data for Bio-Linux packages (...)
20041011-9
BioLinux
Glimmer is a system for finding genes in (...)
3.02-0
BioLinux
Transitional package that provides bio-linux-ncbi-tools-x11 (...)
1:1bl-0
BioLinux
Analysis and visualisation tool for distance data from (...)
4.0-11
BioLinux
Squint is a java-based multiple alignment program and (...)
1.02-2
BioLinux
GenQuery is a set of Perl libraries for (...)
2.2.4-3
BioLinux
STARS is an alternative interface to Staden. (...)
1.2a-11
BioLinux
TaxInspector is a browser for entries in the (...)
1.0b3-10
BioLinux
TETRA - tetranucleotide frequency calculator with GUI. (...)
1.0b3
BioLinux
Graphics, icons, KDE splash screen and a GDM (...)
1.2
BioLinux
Transterm finds rho-independent transcription terminators in bacterial genomes. (...)
2.07-1
BioLinux
Conversion tools for handling conversion of gap format (...)
0.20100408-1
BioLinux
tRNAscan-SE searches for tRNA genes in genomic sequences. (...)
1.23-0
BioLinux
Tutorials and documentation for Bio-Linux users. (...)
1-18
BioLinux
Tool for comparison of biopolymers, DNA, and protein (...)
2.1.20-0
BioLinux
A re-write of the GNU cut command with (...)
1.1-6
BioLinux
Z-Shell wrapper package for Bio-Linux. (...)
1-18
BioLinux
ATV (A Tree Viewer) is a Java tool (...)
1.92-10
BioLinux
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of (...)
2.1.3-0
BioLinux
fastDNAml is a program for estimating maximum likelihood (...)
1:1bl-0
BioLinux
Exchanger lets you store, annotate and share files (...)
1.0-4
BioLinux
Program for detecting coding regions of DNA sequences. (...)
2.1-11
BioLinux
Dust - repetitive sequence masker (...)
1+0.1+20020708-4
BioLinux
Graphical dotplot program for detailed comparison of two (...)
3.1-1
BioLinux
Interactive viewer for large phylogenetic trees. (...)
1.4.0-5
BioLinux
Sets up dependencies necessary for running the DAS (...)
0.1-4
BioLinux
Population estimate modelling. (...)
1.5b-1
BioLinux
Installs clustalw and clustalx for multiple sequence and (...)
1:1bl-6
BioLinux
Conversion tools for handling 454 assemblies. (...)
0.01-9
BioLinux
a suite of programs designed to quickly group (...)
2009-1020-1
BioLinux
A base calling system (...)
20080520-1
BioLinux
Interactive browser for viewing pairwise Blast results. (...)
3.1.1-1
BioLinux
Documentation for bioinformatics software on Bio-Linux. (...)
1.1-96
BioLinux
Blast+ contains new builds of the popular blast (...)
1:1bl1
BioLinux
Rapid searching of nucleotide and protein databases. (...)
1:1bl-6
BioLinux
The big-blast script for annotation of long sequences (...)
1.0.3-4
BioLinux
Essential Bio-Linux configuration files. (...)
1.0-37
CloudBiolinx
Assembly By Short Sequences - a de novo, (...)
1.3.3
CloudBiolinx
BEAST: Bayesian MCMC analysis of molecular sequences. (...)
CloudBiolinx
A flexible suite of utilities for comparing genomic (...)
github
CloudBiolinx
BFAST: Blat-like Fast Accurate Search Tool. (...)
0.7.0
CloudBiolinx
Bio4j graph based database built on Neo4j with (...)
0.7
CloudBiolinx
The bowtie short read aligner. (...)
0.12.7
CloudBiolinx
bowtie2 short read aligner, with gap support. (...)
2.0.0-beta6
bwa
CloudBiolinx
BWA: aligns short nucleotide sequences against a (...)
0.5.9
CloudBiolinx
Tools for manipulating biological data, particularly multiple sequence (...)
bitbucket
CloudBiolinx
Clojure package manager, cljr. (...)
CloudBiolinx
A meta method for installing all of (...)
CloudBiolinx
Detect SNPs and short indels from pooled sequencing (...)
5
CloudBiolinx
Cufflinks assembles transcripts, estimates their abundances, and tests (...)
2.0.0
CloudBiolinx
DWGSIM: simulating NGS data and evaluating mappings and (...)
0.1.8
CloudBiolinx
ECHO: A reference-free short-read error correction algorithm (...)
111
CloudBiolinx
A quality control tool for high throughput sequence (...)
0.10.1
CloudBiolinx
FASTX-Toolkit: collection of command line tools for Short-Reads (...)
0.0.13
CloudBiolinx
Bayesian haplotype-based polymorphism discovery and genotyping. (...)
github
BioLinux
Mesquite is software for evolutionary biology. (...)
2.74-1
CloudBiolinx
Command-line scripting framework for defining multi-stage genomic analysis (...)
1.6-11-g3b2fab9
CloudBiolinx
GMAP and GSNAP: A Genomic Mapping and Alignment (...)
2011-11-12
CloudBiolinx
Hydra detects structural variation breakpoints in both unique (...)
0.5.3
CloudBiolinx
LASTZ sequence alignment program. (...)
1.02.00
CloudBiolinx
Clojure tool for project configuration and automation. (...)
CloudBiolinx
Model-based Analysis for ChIP-Seq. (...)
1.4.2
CloudBiolinx
matplotlib is a python 2D plotting library which (...)
1.0.1
CloudBiolinx
MOSAIK: reference-guided aligner for next-generation sequencing technologies (...)
github
CloudBiolinx
Nginx open source web server. (...)
1.2.0
CloudBiolinx
Novoalign short read aligner using Needleman-Wunsch algorithm with (...)
V2.08.01
CloudBiolinx
Efficient mapping of short sequences accomplished with periodic (...)
3.6
CloudBiolinx
PGDSpider format conversion for population genetics programs. (...)
2.0.1.2
CloudBiolinx
Command-line utilities that manipulate BAM files with a (...)
1.68
CloudBiolinx
A toolset for working with human genetic variation (...)
0.08
CloudBiolinx
Highly configurable GPL-licensed FTP server software. (...)
1.3.4a
CloudBiolinx
pydoop; provides Hadoop access for Python. (...)
rpy
CloudBiolinx
RPy is a very simple, yet robust, Python (...)
1.0.3
CloudBiolinx
FUSE-based file system backed by Amazon S3. (...)
1.61
CloudBiolinx
SAM Tools provide various utilities for manipulating alignments (...)
0.1.18
CloudBiolinx
Install seal: process high-throughput sequencing with Hadoop. (...)
sge
CloudBiolinx
Sun Grid Engine. (...)
CloudBiolinx
Shrec is a bioinformatics tool for error correction (...)
2.2
CloudBiolinx
Variant annotation and effect prediction tool. (...)
205
CloudBiolinx
SolexaQA creates visual representations of data quality from (...)
1.4
CloudBiolinx
Stacks: build loci out of a set of (...)
0.998
CloudBiolinx
Stampy: mapping of short reads from illumina sequencing (...)
1.0.15
CloudBiolinx
TASSEL: evaluate traits associations, evolutionary patterns, and linkage (...)
3.0
CloudBiolinx
TopHat is a fast splice junction mapper for (...)
2.0.0
CloudBiolinx
A program for analysing results from Bayesian MCMC (...)
CloudBiolinx
Analyze ABySS multi-k-assembled shotgun transcriptome data. (...)
1.3.2
CloudBiolinx
Efficient and robust de novo reconstruction of transcriptomes (...)
r2012-05-18
CloudBiolinx
Useful executables from UCSC. (...)
CloudBiolinx
Annotation, selection, and analysis of variants in the (...)
1.0.1
CloudBiolinx
Work with VCF files, such as those generated (...)
0.1.7
CloudBiolinx
Sequence assembler for very short reads. (...)
1.2.05
*) package updates (total & last 90 days) from Debian popularity index as of 2014-04-24