Page History

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

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

k0.7.17-1ubuntu0.1-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

Debian Med bioinformatics applications usable in cloud computing

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 (1.8.0+dfsg-4ubuntu1)?

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 (11.00.8cbe486-6)

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