Page Comparison

2.0.2-3

de novo, parallel, sequence assembler for short reads

bamtools

2.4.1+dfsg-2

toolkit for manipulating BAM (genome alignment) files

bedtools

2.26.0+dfsg-5

suite of utilities for comparing genomic features

1.7.2-2

Perl tools for computational molecular biology

bioperl-run

1.7.1-3

BioPerl wrappers: scripts

1:2.6.0-1

Basic Local Alignment Search Tool

1.2.2+dfsg-2

Ultrafast memory-efficient short read aligner

2.3.4.1-1

Ultrafast memory-efficient short read aligner

0.7.17-1

Burrows-Wheeler Aligner

4.6.8-1

a suite of programs designed to quickly group sequences

clustalw

2.1+lgpl-5

No description

clustalx

2.1+lgpl-6

No description

cufflinks

2.2.1+dfsg.1-2

Transcript assembly, differential expression and regulation for RNA-Seq

ea-utils

1.1.2+dfsg-4build1

command-line tools for processing biological sequencing data

emboss

6.6.0+dfsg-6build1

european molecular biology open software suite

emboss-lib

6.6.0+dfsg-6build1

EMBOSS Libraries

fastdnaml

Tool for construction of phylogenetic trees of DNA sequences

fastqc

0.11.5+dfsg-6

A quality control application for high throughput sequence data

fastx-toolkit

0.0.14-5

FASTQ/A short nucleotide reads pre-processing tools

hmmer

3.1b2+dfsg-5ubuntu1

profile hidden Markov models for protein sequence analysis

jaligner

1.0+dfsg-4

Smith-Waterman algorithm with Gotoh’s improvement

jellyfish

2.2.8-3build1

count k-mers in DNA sequences

khmer

2.1.2+dfsg-3

k-mer counting, filtering and graph traversal

libbiojava-java

1:1.7.1-7

Java API to biological data and applications (default version)

libbiojava-java-demos

1:1.7.1-7

Example programs for BioJava

macs

2.1.1.20160309-2

Model-based Analysis of ChIP-Seq on short reads sequencers

mafft

7.310-1

Multiple alignment program for amino acid or nucleotide sequences

maq

0.7.1-7

maps short fixed-length polymorphic DNA sequence reads to reference sequences

microbiomeutil

20101212+dfsg1-1build1

Microbiome Analysis Utilities

mothur

1.39.5-2build1

sequence analysis suite for research on microbiota

mothur-mpi

1.39.5-2build1

mpi-enabled binary for mothur

mrbayes-mpi

3.2.6+dfsg-2

Bayesian Inference of Phylogeny – mpi version

mummer

3.23+dfsg-3

Efficient sequence alignment of full genomes

muscle

1:3.8.31+dfsg-3

Multiple alignment program of protein sequences

ncbi-blast+

2.6.0-1

next generation suite of BLAST sequence search tools

ncbi-blast+-legacy

2.6.0-1

NCBI Blast legacy call script

ncbi-seg

0.0.20000620-4

tool to mask segments of low compositional complexity in amino acid sequences

ncbi-tools-bin

6.1.20170106-2

NCBI libraries for biology applications (text-based utilities)

ncbi-tools-x11

6.1.20170106-2

NCBI libraries for biology applications (X-based utilities)

paml

4.9g+dfsg-3

Phylogenetic Analysis by Maximum Likelihood (PAML)

parafly

0.0.2013.01.21-3build1

parallel command processing using OpenMP

phylip

1:3.696+dfsg-5

No description

phyml

3:3.3.20170530+dfsg-2

Phylogenetic estimation using Maximum Likelihood

picard-tools

2.8.1+dfsg-3

Command line tools to manipulate SAM and BAM files

primer3

2.4.0-1ubuntu2

Tool to design flanking oligo nucleotides for DNA amplification

pymol

1.8.4.0+dfsg-1build1

Molecular Graphics System

qiime

3:3.3.20170530+dfsg-2

Quantitative Insights Into Microbial Ecology

rasmol

2.7.5.2-2

Visualize biological macromolecules

raxml

8.2.11+dfsg-1

Randomized Axelerated Maximum Likelihood of phylogenetic trees

readseq

1-12

Conversion between sequence formats

rsem

1.2.31+dfsg-1

RNA-Seq by Expectation-Maximization

samtools

1.7-1

processing sequence alignments in SAM and BAM formats

sift

4.0.3b-6

predicts if a substitution in a protein has a phenotypic effect

sortmerna

2.1-2

tool for filtering, mapping and OTU-picking NGS reads

stacks

2.0Beta8c+dfsg-1

pipeline for building loci from short-read sequences

sumatra

1.0.31-1

fast and exact comparison and clustering of sequences

swarm

2.2.2+dfsg-1

robust and fast clustering method for amplicon-based studies

t-coffee

2.2.2+dfsg-1

Multiple Sequence Alignment

tophat

2.1.1+dfsg1-1

fast splice junction mapper for RNA-Seq reads

transdecoder

5.0.1-1

find coding regions within transcripts

trinityrnaseq

2.5.1+dfsg-2

RNA-Seq De novo Assembly

trnascan-se

1.3.1-1

search for tRNA genes in genomic sequences

velvet

1.2.10+dfsg1-3build1

Nucleic acid sequence assembler for very short reads

velvet-example

1.2.10+dfsg1-3build1

Example data for the Velvet sequence assembler

velvet-long

1.2.10+dfsg1-3build1

Nucleic acid sequence assembler for very short reads, long version

velvetoptimiser

2.2.6-1

Automatically optimise Velvet do novo assembly parameters

vsearch

2.7.1-1

tool for processing metagenomic sequences

GNU R package “Combine multi-dimensional arrays”

ade4

GNU R package “Analysis of Ecological Data : Exploratory

GNU R package “Analyses of Phylogenetics and Evolution”

bitops

GNU R package implementing bitwise operations

catools

GNU R package “Tools: moving window statistics, GIF,

cluster

GNU R package for cluster analysis by Rousseeuw et al

data.table

GNU R package “Extension of data.frame”

dbi

GNU R package “R Database Interface”

dichromat

Color schemes for dichromats

digest

GNU R package “Create Cryptographic Hash Digests of R

evaluate

GNU R package “Parsing and Evaluation Tools that Provide

futile.logger

GNU R package “A Logging Utility for R”

futile.options

GNU R package “Futile options management”

gdata

GNU R package “Various R Programming Tools for Data

getopt

GNU R package “C-like getopt behavior.”

ggplot2

GNU R package “An Implementation of the Grammar of

gplots

GNU R package “Various R Programming Tools for Plotting

gtable

GNU R package “Arrange grobs in tables.”

gtools

GNU R package “Various R Programming Tools”

labeling

GNU R package “Axis Labeling”

lambda.r

GNU R package “Modeling Data with Functional Programming”

lattice

GNU R package “Lattice Graphics”

GNU R package “regression subset selection”

GNU R package for linear mixed effects model fitting

matrix

GNU R package of classes for dense and sparse matrices

matrixstats

R package “Methods that apply to rows and columns of a matrix”

munsell

GNU R package “Munsell colour system”

nlme

GNU R package for (non-)linear mixed effects models

optparse

GNU R package “Command line option parser.”

permute

GNU R package “Functions for Generating Restricted

GNU R package “Various plotting functions”

plyr

GNU R package “Tools for Splitting, Applying and Combining

proto

GNU R package “Prototype object-based programming”

r.methodss3

GNU R package “Utility function for defining S3 methods”

rcolorbrewer

GNU R package providing suitable color palettes

rcpp

GNU R package “Seamless R and C++ Integration”

rcurl

GNU R package “General Network (HTTP/FTP/…) Client

relimp

GNU R package “Relative Contribution of Effects in a

reshape2

GNU R package “Flexibly Reshape Data: A Reboot of the

rggobi

GNU R package for the GGobi data visualization system

rgl

GNU R package for three-dimensional visualisation using OpenGL

rgtk2

GNU R binding for Gtk2

rmpi

GNU R package interfacing MPI libraries for distributed computing

rserve

GNU R Rserve tcp/ip server and sample clients

rsqlite

GNU R package “SQLite Interface for R”

scales

GNU R package “Scale Functions for Visualization”

scatterplot3d

GNU R package “3D Scatter Plot”

sp

GNU R package “Classes and Methods for Spatial Data”

stringr

GNU R package “Simple, Consistent Wrappers for Common

tcltk2

GNU R package “Tcl/Tk Additions”

testthat

GNU R package “Testthat code. Tools to make testing fun

vegan

GNU R package “Community Ecology Package”

xml

GNU R package “Tools for Parsing and Generating XML Within

xtable

GNU R coerce data to LaTeX and HTML tables

GNU R package “Tools for parsing Affymetrix data files”

GNU R package “Annotation for microarrays”

annotationdbi

GNU R package “Annotation Database Interface”

GNU R package “Biobase: Base functions for Bioconductor”

biocgenerics

GNU R package “S4 generic functions for Bioconductor”

biocinstaller

GNU R package “Install/Update Bioconductor and CRAN

biocparallel

GNU R package “Bioconductor facilities for parallel

biomart

GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene)

biostrings

GNU R package “String objects representing biological

Collection of package development tools

GNU R package “genefilter: methods for filtering genes

geneplotter

Graphics related functions for Bioconductor

genomeinfodb

GNU R package “Utilities for manipulating chromosome and

genomicalignments

GNU R package “Representation and manipulation of short

genomicranges

GNU R package “Representation and manipulation of genomic

hilbertvis

GNU R package to visualise long vector data

iranges

GNU R package “Infrastructure for manipulating intervals

limma

GNU R package “Linear Models for Microarray Data”

multtest

GNU R package “Resampling-based multiple hypothesis

preprocesscore

GNU R package “A collection of pre-processing functions”

Bioconductor package “Q-value estimation for false discovery rate control”

provides an interface between HDF5 and R

GNU R package “Binary alignment (BAM), variant call (BCF),

s4vectors

GNU R package “S4 implementation of vectors and lists”

xvector

GNU R package “Representation and manpulation of external

zlibbioc

GNU R package “An R packaged zlib-1.2.5″