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Let us know if there is additional software you would like to have installed.
Standard OS Software (where in repo?)
| Software | Description |
|---|---|
| build-essential | gcc, g++, make, cmake, patch, autoconf, automake, m4, bison, libtool |
| emacs, vi, vim, ed | text editors |
| postfix | mail programs |
| perl | perl interpretor |
| python 2 | python version 2 interpretor |
| python 3 | python version 3 interpretor |
| ruby | ruby programming language |
| samba | Windows SMB/CIFS file and printer sharing protocol and applications |
| screen, tmux | Text window managers (multiplexer) |
| ssh | Secure Shell (remote access) |
| sudo | Root access for POD delegates only |
| tar | File archiving utility |
| wget, curl | Remote file/url transfer utilities |
| gzip, zip, unzip | File compression and archiving tools. |
Standard BioLinux Packages (
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how check versions)
| Software | Version | Description | in cqb-biolinux? |
|---|---|---|---|
2.0.2-3 | de novo, parallel, sequence assembler for short reads | y | |
bamtools | 2.4.1+dfsg-2 | toolkit for manipulating BAM (genome alignment) files | y |
bedtools | 2.26.0+dfsg-5 | suite of utilities for comparing genomic features | y |
| bioperl | 1.7.2-2 | Perl tools for computational molecular biology | y |
bioperl-run | 1.7.1-3 | BioPerl wrappers: scripts | y |
| blast2 | 1:2.6.0-1 | Basic Local Alignment Search Tool | y |
| bowtie | 1.2.2+dfsg-2 | Ultrafast memory-efficient short read aligner | y |
| bowtie2 | 2.3.4.1-1 | Ultrafast memory-efficient short read aligner | n |
| bwa | 0.7.17-1 | Burrows-Wheeler Aligner | n |
| cd-hit | 4.6.8-1 | a suite of programs designed to quickly group sequences | y |
clustalw | 2.1+lgpl-5 | No description | y |
clustalx | 2.1+lgpl-6 | No description | y |
cufflinks | 2.2.1+dfsg.1-2 | Transcript assembly, differential expression and regulation for RNA-Seq | n |
ea-utils | 1.1.2+dfsg-4build1 | command-line tools for processing biological sequencing data | y |
emboss | 6.6.0+dfsg-6build1 | european molecular biology open software suite | n |
emboss-lib | 6.6.0+dfsg-6build1 | EMBOSS Libraries | y |
fastdnaml | 1.2.2-12 | Tool for construction of phylogenetic trees of DNA sequences | y |
fastqc | 0.11.5+dfsg-6 | A quality control application for high throughput sequence data | n |
fastx-toolkit | 0.0.14-5 | FASTQ/A short nucleotide reads pre-processing tools | y |
hmmer | 3.1b2+dfsg-5ubuntu1 | profile hidden Markov models for protein sequence analysis | n |
jaligner | 1.0+dfsg-4 | Smith-Waterman algorithm with Gotoh’s improvement | y |
jellyfish | 2.2.8-3build1 | count k-mers in DNA sequences | y |
khmer | 2.1.2+dfsg-3 | k-mer counting, filtering and graph traversal | y |
libbiojava-java | 1:1.7.1-7 | Java API to biological data and applications (default version) | y |
libbiojava-java-demos | 1:1.7.1-7 | Example programs for BioJava | y |
macs | 2.1.1.20160309-2 | Model-based Analysis of ChIP-Seq on short reads sequencers | y |
mafft | 7.310-1 | Multiple alignment program for amino acid or nucleotide sequences | y |
maq | 0.7.1-7 | maps short fixed-length polymorphic DNA sequence reads to reference sequences | y |
| med-bio | y | ||
| med-cloud | y | ||
microbiomeutil | 20101212+dfsg1-1build1 | Microbiome Analysis Utilities | y |
mothur | 1.39.5-2build1 | sequence analysis suite for research on microbiota | y |
mothur-mpi | 1.39.5-2build1 | mpi-enabled binary for mothur | y |
mrbayes-mpi | 3.2.6+dfsg-2 | Bayesian Inference of Phylogeny – mpi version | y |
mummer | 3.23+dfsg-3 | Efficient sequence alignment of full genomes | y |
muscle | 1:3.8.31+dfsg-3 | Multiple alignment program of protein sequences | y |
ncbi-blast+ | 2.6.0-1 | next generation suite of BLAST sequence search tools | n |
ncbi-blast+-legacy | 2.6.0-1 | NCBI Blast legacy call script | n |
ncbi-seg | 0.0.20000620-4 | tool to mask segments of low compositional complexity in amino acid sequences | y |
ncbi-tools-bin | 6.1.20170106-2 | NCBI libraries for biology applications (text-based utilities) | y |
ncbi-tools-x11 | 6.1.20170106-2 | NCBI libraries for biology applications (X-based utilities) | y |
paml | 4.9g+dfsg-3 | Phylogenetic Analysis by Maximum Likelihood (PAML) | y |
parafly | 0.0.2013.01.21-3build1 | parallel command processing using OpenMP | y |
phylip | 1:3.696+dfsg-5 | No description | y |
phyml | 3:3.3.20170530+dfsg-2 | Phylogenetic estimation using Maximum Likelihood | y |
picard-tools | 2.8.1+dfsg-3 | Command line tools to manipulate SAM and BAM files | y |
primer3 | 2.4.0-1ubuntu2 | Tool to design flanking oligo nucleotides for DNA amplification | y |
pymol | 1.8.4.0+dfsg-1build1 | Molecular Graphics System | y |
qiime | 3:3.3.20170530+dfsg-2 | Quantitative Insights Into Microbial Ecology | y |
rasmol | 2.7.5.2-2 | Visualize biological macromolecules | y |
raxml | 8.2.11+dfsg-1 | Randomized Axelerated Maximum Likelihood of phylogenetic trees | y |
readseq | 1-12 | Conversion between sequence formats | y |
rsem | 1.2.31+dfsg-1 | RNA-Seq by Expectation-Maximization | y |
samtools | 1.7-1 | processing sequence alignments in SAM and BAM formats | n |
sift | 4.0.3b-6 | predicts if a substitution in a protein has a phenotypic effect | y |
sortmerna | 2.1-2 | tool for filtering, mapping and OTU-picking NGS reads | y |
stacks | 2.0Beta8c+dfsg-1 | pipeline for building loci from short-read sequences | y |
sumatra | 1.0.31-1 | fast and exact comparison and clustering of sequences | y |
swarm | 2.2.2+dfsg-1 | robust and fast clustering method for amplicon-based studies | y |
t-coffee | 2.2.2+dfsg-1 | Multiple Sequence Alignment | n |
tophat | 2.1.1+dfsg1-1 | fast splice junction mapper for RNA-Seq reads | n |
transdecoder | 5.0.1-1 | find coding regions within transcripts | y |
trinityrnaseq | 2.5.1+dfsg-2 | RNA-Seq De novo Assembly | y |
trnascan-se | 1.3.1-1 | search for tRNA genes in genomic sequences | y |
velvet | 1.2.10+dfsg1-3build1 | Nucleic acid sequence assembler for very short reads | y |
velvet-example | 1.2.10+dfsg1-3build1 | Example data for the Velvet sequence assembler | y |
velvet-long | 1.2.10+dfsg1-3build1 | Nucleic acid sequence assembler for very short reads, long version | y |
velvetoptimiser | 2.2.6-1 | Automatically optimise Velvet do novo assembly parameters | y |
vsearch | 2.7.1-1 | tool for processing metagenomic sequences | y |
| zsh | y |
Standard Third-Party Software (versions?)
| Software | Description |
|---|---|
| R, Rscript | R command-line shell and script execution programs. |
| Matlab | MathWorks Matlab Software. See How do I use MATLAB on the POD? |
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Additional Python Tools (devel tools)
| Software | Description | in devel_tools |
|---|---|---|
| all-dev | y | |
| blaze | An interface to query data on different storage systems | y |
| cutadapt | Finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads | y |
| dendropy | phylogenetic computing | y |
| freetype-dev (libfreetype6-dev) | y | |
| leukgen-disambiguate | y | |
| MACS2 | Model Based Analysis for ChIP-Seq data | y |
| maplot | y | |
| matplotlib | python 2D plotting library | y |
| networkx | Creation, manipulation, and study of the structure, dynamics, and functions of complex networks. | y |
| nimfa | Nonnegative matrix factorization | y |
| numpy | scientific computing with Python | y |
| pandas | Python Data Analysis Library | y |
| patsy | y | |
| pip | Python installation program (to install python modules) | y |
| plotly | y | |
| pysam | y | |
| pyvttbl | y | |
| reportlab (->biopython?) | y | |
| rpy2 | Python interface to R | y |
| seaborn | y | |
| scipy | Collection of Python software for mathematics, science, and engineering. | y |
| sklearn | Machine Learning in Python | y |
| skimage | Image processing in Python | y |
| statsmodels | Estimation of statistical models | y |
Additional R Tools (r_client.pp)
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