biogems.info

Important software packages installed and tested on CloudBiolinux

#	package (.deb)	origin	description	version	pop*)
1	rasmol	Debian	Visualize biological macromolecules (...)	2.7.5-3	284
2	treeviewx	Debian	Displays and prints phylogenetic trees (...)	0.5.1+20100823-1	126
3	clustalx	Debian	Multiple alignment of nucleic acid and protein sequences (...)	2.1+lgpl-2	96
4	blast2	Debian	Basic Local Alignment Search Tool (...)	1:2.2.25.20110713-3ubuntu2	64
5	emboss	Debian	the european molecular biology open software suite (...)	6.3.1-6ubuntu3	45
6	muscle	Debian	Multiple alignment program of protein sequences (...)	1:3.8.31-1	37
7	primer3	Debian	Tool to design flanking oligo nucleotides for DNA (...)	2.2.3-1	35
8	phyml	Debian	Phylogenetic estimation using Maximum Likelihood (...)	2:20110919-1	32
9	dialign	Debian	Segment-based multiple sequence alignment (...)	2.2.1-5	31
10	mafft	Debian	Multiple alignment program for amino acid or nucleotide (...)	6.850-1	31
11	hmmer	Debian	profile hidden Markov models for protein sequence analysis (...)	3.0-3	30
12	t coffee	Debian	Multiple Sequence Alignment (...)	8.99-1	28
13	exonerate	Debian	generic tool for pairwise sequence comparison (...)	2.2.0-6	27
14	mummer	Debian	Efficient sequence alignment of full genomes (...)	3.22~dfsg-2	26
15	probcons	Debian	PROBabilistic CONSistency-based multiple sequence alignment (...)	1.12-8	25
16	ncbi blast+	Debian	next generation suite of BLAST sequence search tools (...)	2.2.25-7	22
17	mcl	Debian	Markov Cluster algorithm (...)	1:11-294-1	17
18	phylip	Debian	package of programs for inferring phylogenies (...)	1:3.69-1	12
19	mrbayes	Debian	Bayesian Inference of Phylogeny (...)	3.1.2-2	8
20	bio linux mrbayes multi	BioLinux	Multiprocessor version of MrBayes (...)	3.1.2-4	2
21	bio linux ncbi tools x11	BioLinux	NCBI libraries for biology applications (X-based utilities) (...)	1:1bl-2	2
22	bio linux clcsequenceviewer	BioLinux	CLC Free Sequence Viewer (...)	6.4-1	1
23	bio linux fasta	BioLinux	Collection of programs for searching DNA and protein (...)	36t2d5-0	1
24	bio linux treeview	BioLinux	TreeView is a simple program for displaying phylogenies. (...)	1:1bl-0	1
25	bio linux staden	BioLinux	A suite of tools for sequence analysis. (...)	2006.1.7.0+1.11.6-5	1
26	bio linux seaview	BioLinux	Multiple sequence alignment editor. (...)	4.2.8-2	1
27	bio linux fluctuate	BioLinux	Population modelling software. (...)	1.4-0	1
28	bio linux jalview	BioLinux	Jalview is a Java multiple alignment editor (...)	1:2.6.1-1	1
29	ugene	Debian	integrated bioinformatics toolkit (...)	1.9.8+repack-0ubuntu3	1
30	bio linux lucy	BioLinux	Preparation of raw DNA sequence fragments for sequence (...)	1.20-0	1
31	bio linux maxd	BioLinux	maxd is a data warehouse and visualisation environment (...)	2.3.0-5	1
32	gatk	CloudBiolinx	GATK: library for writing efficient analysis tools using (...)	1.6-11-g3b2fab9
33	bio linux migrate	BioLinux	Estimates effective population sizes and past migration rates (...)	3.1.2-1
34	bio linux keyring	BioLinux	Public key package for the Bio-Linux package repository (...)	4
35	bio linux mspcrunch	BioLinux	MSPcrunch is a BLAST post-processing filter. (...)	2.5-0
36	bio linux mview	BioLinux	Multiple alignment viewer for sequence database search results. (...)	1.51-2
37	bio linux happy	BioLinux	HAPPY: a software package for Multipoint QTL Mapping (...)	1.2-1
38	bio linux nrdb	BioLinux	nrdb can be used to generate quasi-nonredundant protein (...)	2-0
39	bio linux ocount	BioLinux	Ocount - oligonucleotide frequency counter. (...)	0.5-0
40	bio linux oligoarray	BioLinux	Computation of gene-specific oligonucleotides for genome-scale microarray construction. (...)	2.1-8
41	bio linux oligoarrayaux	BioLinux	OligoArrayAux 3.7 is free software that is required (...)	3.7-0
42	bio linux omegamap	BioLinux	OmegaMap is a program for detecting natural selection (...)	0.5-0
43	bio linux paml	BioLinux	Phylogenetic analysis tool for DNA and protein sequences (...)	4.4c-1
44	bio linux partigene	BioLinux	Cluster and anotation tool for sequence data. (...)	3.05-8
45	bio linux pfaat	BioLinux	Sequence alignment editor designed for protein family analysis. (...)	1.0.034-5
46	bio linux prank	BioLinux	Multiple alignment software. (...)	20100318-0
47	bio linux prevent upgrade	BioLinux	Stop Bio-Linux from upgrading on release of 12.04 (...)	0.2
48	bio linux prot4est	BioLinux	Translation of error-prone nucleotide sequences producing robust polypeptide (...)	2.2-10
49	bio linux qtlcart	BioLinux	Suite of programs to map quantitative traits using (...)	1.17f-0
50	bio linux rbs finder	BioLinux	A program to find Ribosomal binding sites. (...)	1.0-3
51	bio linux recombine	BioLinux	Population modelling software. (...)	1.41-0
52	bio linux sampledata	BioLinux	Sample data for Bio-Linux packages (...)	20041011-9
53	bio linux glimmer3	BioLinux	Glimmer is a system for finding genes in (...)	3.02-0
54	bio linux sequin	BioLinux	Transitional package that provides bio-linux-ncbi-tools-x11 (...)	1:1bl-0
55	bio linux splitstree	BioLinux	Analysis and visualisation tool for distance data from (...)	4.0-11
56	bio linux squint	BioLinux	Squint is a java-based multiple alignment program and (...)	1.02-2
57	bio linux genquery	BioLinux	GenQuery is a set of Perl libraries for (...)	2.2.4-3
58	bio linux stars	BioLinux	STARS is an alternative interface to Staden. (...)	1.2a-11
59	bio linux taxinspector	BioLinux	TaxInspector is a browser for entries in the (...)	1.0b3-10
60	bio linux tetra	BioLinux	TETRA - tetranucleotide frequency calculator with GUI. (...)	1.0b3
61	bio linux themes v5	BioLinux	Graphics, icons, KDE splash screen and a GDM (...)	1.2
62	bio linux transterm hp	BioLinux	Transterm finds rho-independent transcription terminators in bacterial genomes. (...)	2.07-1
63	bio linux gap2caf	BioLinux	Conversion tools for handling conversion of gap format (...)	0.20100408-1
64	bio linux trnascan	BioLinux	tRNAscan-SE searches for tRNA genes in genomic sequences. (...)	1.23-0
65	bio linux tutorials	BioLinux	Tutorials and documentation for Bio-Linux users. (...)	1-18
66	bio linux wise2	BioLinux	Tool for comparison of biopolymers, DNA, and protein (...)	2.1.20-0
67	bio linux xcut	BioLinux	A re-write of the GNU cut command with (...)	1.1-6
68	bio linux zsh	BioLinux	Z-Shell wrapper package for Bio-Linux. (...)	1-18
69	bio linux forester	BioLinux	ATV (A Tree Viewer) is a Java tool (...)	1.92-10
70	bio linux fasttree	BioLinux	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of (...)	2.1.3-0
71	bio linux fastdnaml	BioLinux	fastDNAml is a program for estimating maximum likelihood (...)	1:1bl-0
72	bio linux exchanger	BioLinux	Exchanger lets you store, annotate and share files (...)	1.0-4
73	bio linux estscan	BioLinux	Program for detecting coding regions of DNA sequences. (...)	2.1-11
74	bio linux dust	BioLinux	Dust - repetitive sequence masker (...)	1+0.1+20020708-4
75	bio linux dotter	BioLinux	Graphical dotplot program for detailed comparison of two (...)	3.1-1
76	bio linux dendroscope	BioLinux	Interactive viewer for large phylogenetic trees. (...)	1.4.0-5
77	bio linux das prep	BioLinux	Sets up dependencies necessary for running the DAS (...)	0.1-4
78	bio linux coalesce	BioLinux	Population estimate modelling. (...)	1.5b-1
79	bio linux clustal	BioLinux	Installs clustalw and clustalx for multiple sequence and (...)	1:1bl-6
80	bio linux assembly conversion tools	BioLinux	Conversion tools for handling 454 assemblies. (...)	0.01-9
81	bio linux cd hit	BioLinux	a suite of programs designed to quickly group (...)	2009-1020-1
82	bio linux cap3	BioLinux	A base calling system (...)	20080520-1
83	bio linux blixem	BioLinux	Interactive browser for viewing pairwise Blast results. (...)	3.1.1-1
84	bio linux bldp files	BioLinux	Documentation for bioinformatics software on Bio-Linux. (...)	1.1-96
85	bio linux blast+	BioLinux	Blast+ contains new builds of the popular blast (...)	1:1bl1
86	bio linux blast	BioLinux	Rapid searching of nucleotide and protein databases. (...)	1:1bl-6
87	bio linux big blast	BioLinux	The big-blast script for annotation of long sequences (...)	1.0.3-4
88	bio linux base directories	BioLinux	Essential Bio-Linux configuration files. (...)	1.0-37
89	abyss	CloudBiolinx	Assembly By Short Sequences - a de novo, (...)	1.3.3
90	beast	CloudBiolinx	BEAST: Bayesian MCMC analysis of molecular sequences. (...)
91	bedtools	CloudBiolinx	A flexible suite of utilities for comparing genomic (...)	github
92	bfast	CloudBiolinx	BFAST: Blat-like Fast Accurate Search Tool. (...)	0.7.0
93	bio4j	CloudBiolinx	Bio4j graph based database built on Neo4j with (...)	0.7
94	bowtie	CloudBiolinx	The bowtie short read aligner. (...)	0.12.7
95	bowtie2	CloudBiolinx	bowtie2 short read aligner, with gap support. (...)	2.0.0-beta6
96	bwa	CloudBiolinx	BWA: aligns short nucleotide sequences against a (...)	0.5.9
97	bx python	CloudBiolinx	Tools for manipulating biological data, particularly multiple sequence (...)	bitbucket
98	cljr	CloudBiolinx	Clojure package manager, cljr. (...)
99	cloudman	CloudBiolinx	A meta method for installing all of (...)
100	crisp	CloudBiolinx	Detect SNPs and short indels from pooled sequencing (...)	5
101	cufflinks	CloudBiolinx	Cufflinks assembles transcripts, estimates their abundances, and tests (...)	2.0.0
102	dwgsim	CloudBiolinx	DWGSIM: simulating NGS data and evaluating mappings and (...)	0.1.8
103	echo	CloudBiolinx	ECHO: A reference-free short-read error correction algorithm (...)	1_11
104	fastqc	CloudBiolinx	A quality control tool for high throughput sequence (...)	0.10.1
105	fastx toolkit	CloudBiolinx	FASTX-Toolkit: collection of command line tools for Short-Reads (...)	0.0.13
106	freebayes	CloudBiolinx	Bayesian haplotype-based polymorphism discovery and genotyping. (...)	github
107	bio linux mesquite	BioLinux	Mesquite is software for evolutionary biology. (...)	2.74-1
108	gatk queue	CloudBiolinx	Command-line scripting framework for defining multi-stage genomic analysis (...)	1.6-11-g3b2fab9
109	gmap	CloudBiolinx	GMAP and GSNAP: A Genomic Mapping and Alignment (...)	2011-11-12
110	hydra	CloudBiolinx	Hydra detects structural variation breakpoints in both unique (...)	0.5.3
111	lastz	CloudBiolinx	LASTZ sequence alignment program. (...)	1.02.00
112	leinengin	CloudBiolinx	Clojure tool for project configuration and automation. (...)
113	macs	CloudBiolinx	Model-based Analysis for ChIP-Seq. (...)	1.4.2
114	matplotlib	CloudBiolinx	matplotlib is a python 2D plotting library which (...)	1.0.1
115	mosaik	CloudBiolinx	MOSAIK: reference-guided aligner for next-generation sequencing technologies (...)	github
116	nginx	CloudBiolinx	Nginx open source web server. (...)	1.2.0
117	novoalign	CloudBiolinx	Novoalign short read aligner using Needleman-Wunsch algorithm with (...)	V2.08.01
118	perm	CloudBiolinx	Efficient mapping of short sequences accomplished with periodic (...)	3.6
119	pgdspider	CloudBiolinx	PGDSpider format conversion for population genetics programs. (...)	2.0.1.2
120	picard	CloudBiolinx	Command-line utilities that manipulate BAM files with a (...)	1.68
121	plink seq	CloudBiolinx	A toolset for working with human genetic variation (...)	0.08
122	proftpd	CloudBiolinx	Highly configurable GPL-licensed FTP server software. (...)	1.3.4a
123	pydoop	CloudBiolinx	pydoop; provides Hadoop access for Python. (...)
124	rpy	CloudBiolinx	RPy is a very simple, yet robust, Python (...)	1.0.3
125	s3fs	CloudBiolinx	FUSE-based file system backed by Amazon S3. (...)	1.61
126	samtools	CloudBiolinx	SAM Tools provide various utilities for manipulating alignments (...)	0.1.18
127	seal	CloudBiolinx	Install seal: process high-throughput sequencing with Hadoop. (...)
128	sge	CloudBiolinx	Sun Grid Engine. (...)
129	shrec	CloudBiolinx	Shrec is a bioinformatics tool for error correction (...)	2.2
130	snpeff	CloudBiolinx	Variant annotation and effect prediction tool. (...)	2_0_5
131	solexaqa	CloudBiolinx	SolexaQA creates visual representations of data quality from (...)	1.4
132	stacks	CloudBiolinx	Stacks: build loci out of a set of (...)	0.998
133	stampy	CloudBiolinx	Stampy: mapping of short reads from illumina sequencing (...)	1.0.15
134	tassel	CloudBiolinx	TASSEL: evaluate traits associations, evolutionary patterns, and linkage (...)	3.0
135	tophat	CloudBiolinx	TopHat is a fast splice junction mapper for (...)	2.0.0
136	tracer	CloudBiolinx	A program for analysing results from Bayesian MCMC (...)
137	transabyss	CloudBiolinx	Analyze ABySS multi-k-assembled shotgun transcriptome data. (...)	1.3.2
138	trinity	CloudBiolinx	Efficient and robust de novo reconstruction of transcriptomes (...)	r2012-05-18
139	ucsc tools	CloudBiolinx	Useful executables from UCSC. (...)
140	varianttools	CloudBiolinx	Annotation, selection, and analysis of variants in the (...)	1.0.1
141	vcftools	CloudBiolinx	Work with VCF files, such as those generated (...)	0.1.7
142	velvet	CloudBiolinx	Sequence assembler for very short reads. (...)	1.2.05

*) package updates (total & last 90 days) from Debian popularity index as of 2013-05-22