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这篇文章主要为大家展示了“Bio-Linux中的生物信息学软件有哪些”，内容简而易懂，条理清晰，希望能够帮助大家解决疑惑，下面让小编带领大家一起研究并学习一下“Bio-Linux中的生物信息学软件有哪些”这篇文章吧。
Bio-Linux是功能齐全的、强大的、可定制的、易于维护的生物分析工作站。Bio-Linux基于Ubuntu提供500多个生物分析程序，由一个 图形化的菜单进行管理，能方便地访问到其生物分析文档系统及对测试程序有用的样本数据。用于处理新型序列数据类型的Bio-Linux软件包可额外安装。
下面是我们我们打包好的bolinux的ova包，在根目录下的biosoft文件夹下有增加的软件。
链接：https://pan.baidu.com/s/1ui9ndOsjbtgHrJoxxOcTMQ
系统用户及密码：
用户：manager 密码：manager 用户：root 密码：manager
组学大讲堂安装的软件列表，见安装目录 /biosoft：
annovar
annovar2016_06_24
BreakDancer
circos
e-PCR
GATK
java
meme
miniconda
MISA
Primer3
rpm
sratoolkit
vcftools
Bio-Linux中有很多安装的生物信息学软件，这里给大家列举一下：
原版下载地址：http://environmentalomics.org/bio-linux/
Package abyss | Version 1.9.0 | Description de novo, parallel, sequence assembler for short reads |
| ampliconnoise | 1.29 | Programs for the removal of noise from 454 sequenced PCR amplicons |
| arb | 5.5 | No description |
| archaeopteryx | 0.972.beta9M | A phylogenetic tree viewer and editor |
| artemis | 16.0.0 | Free genome viewer and annotation tool |
| assembly-conversion-tools | 0.01 | Conversion tools for handling 454 assemblies. |
| axiome | 1.7biolinux1 | QIIME and mothur automation toolkit |
| axiome-dev | 1.7biolinux1 | QIIME automation toolkit — Plugin Development |
| backups | 0.3 | Bio-Linux 5/6/7 backup utilities. |
| bamtools | 2.4.0+dfsg | toolkit for manipulating BAM (genome alignment) files |
| beam2 | 0.1+20101008 | SNP-SNP interaction association mapping based on SNP-block models |
| bedtools | 2.17.0 | suite of utilities for comparing genomic features |
| berkeley-express | 1.5.1 | Streaming quantification for high-throughput sequencing |
| big-blast | 1.0.3 | The big-blast script for annotation of long sequences |
| biocode | 2.3.3 | Biocode plugin for Geneious workbench |
| bioperl | 1.6.923 | Perl tools for computational molecular biology |
| bioperl-run | 1.6.9 | BioPerl wrappers: scripts |
| biosquid | 1.9g+cvs20050121 | utilities for biological sequence analysis |
| bitseq | 0.7.0 | Bayesian Inference of Transcripts from Sequencing Data |
| blast2 | 1:2.2.26.20120620 | Basic Local Alignment Search Tool |
| bldp-files | 1.1 | Documentation for bioinformatics software on Bio-Linux. |
| blimps-utils | 3.9 | blocks database improved searcher |
| blixem | 3.1.1 | Interactive browser for viewing pairwise Blast results. |
| bowtie | 1.1.1 | Ultrafast memory-efficient short read aligner |
| bowtie2 | 2.2.6 | ultrafast memory-efficient short read aligner |
| bowtie2-debug | 2.2.6 | ultrafast memory-efficient short read aligner |
| bwa | 0.7.12 | Burrows-Wheeler Aligner |
| cap3 | 20080520 | A base calling system |
| catchall | 3.0.1 | Analyze data about microbial species abundance |
| cd-hit | 2009-1020 | a suite of programs designed to quickly group sequences |
| cdbfasta | 20100722 | Constant DataBase indexing and retrieval tools for multi-FASTA files |
| chimeraslayer | 20101212+dfsg | detects likely chimeras in PCR amplified DNA |
| clcsequenceviewer | 6.4 | CLC Free Sequence Viewer |
| clearcut | 1.0.9 | Relaxed Neighbor Joining |
| clustalw | 2.1+lgpl | No description |
| clustalx | 2.1+lgpl | No description |
| cortex-con | 0.05 | efficient and low-memory software for consensus genome assembly |
| cruft-killer | 0.3 | Remove cruft from Bio-Linux desktop |
| cufflinks | 2.2.1 | Transcript assembly, differential expression and regulation for RNA-Seq |
| cytoscape | 1:3.2.1 | Platform for visualizing complex-networks and integrating these with attribute data |
| dendroscope | 1.4.0 | Interactive viewer for large phylogenetic trees. |
| dialign | 2.2.1 | Segment-based multiple sequence alignment |
| dotter | 3.1 | Graphical dotplot program for detailed comparison of two sequences |
| ea-utils | 1.1.2+dfsg | command-line tools for processing biological sequencing data |
| embassy-domainatrix | 0.1.650 | Extra EMBOSS commands to handle domain classification file |
| embassy-domalign | 0.1.650 | Extra EMBOSS commands for protein domain alignment |
| embassy-domsearch | 1:0.1.650 | Extra EMBOSS commands to search for protein domains |
| embassy-phylip | 3.69.650 | No description |
| emboss | 6.6.0+dfsg | european molecular biology open software suite |
| emboss-lib | 6.6.0+dfsg | EMBOSS Libraries |
| estscan2 | 2.1 | detects coding regions of DNA sequences |
| exchanger | 1.0 | lets you store, annotate and share files via an omixed server |
| fasta | 36t2d5 | Collection of programs for searching DNA and protein databases. |
| fastdnaml | 1.2.2 | Tool for construction of phylogenetic trees of DNA sequences |
| fastqc | 0.11.3 | A quality control application for high throughput sequence data |
| fasttree | 2.1.7 | phylogenetic trees from alignments of nucleotide or protein sequences |
| fastx-toolkit | 0.0.14 | FASTQ/A short nucleotide reads pre-processing tools |
| fixups | 8.0 | Miscellanous fixups for Bio-Linux |
| fraggenescan | 1.19 | finds (fragmented) genes in short reads |
| galaxy-server | 1.bl.py27.20140730 | Web-based analysis environment for bioinformatics |
| galaxy-server-apache-proxy | 1.bl.py27.20140730 | Activates Apache2 proxy for Galaxy server, and PAM authentication |
| galaxy-server-pg-database | 1.bl.py27.20140730 | Activates PostgreSQL database back-end for Galaxy |
| galaxy-tools-bl | 1:0.5.1 | Standard set of tool wrappers for Galaxy server |
| gap2caf | 0.20100408 | Handles conversion of gap format assemblies to caf format. |
| geneious | 5.5.7 | Geneious Basic workbench from Biomatters |
| geneious-genbanksubmit | 1.3.0 | GenBank submission for Geneious workbench |
| genquery | 2.2.4 | GenQuery is a set of Perl libraries for managing SQL query templates and making web-based query forms. |
| glam2 | 1:4.10.0.1 | gapped protein motifs from unaligned sequences |
| glimmer3 | 3.02 | Gene detection in archea and bacteria |
| gnx-tools | 0.1+20120305 | Basic genome assembly statistic tool to calculate Nx values e.g. N50,N10,NG50 |
| handlebar | 2.2.2 | Handlebar is a database for storing data about barcodes and acessing the data via a web front-end. |
| happy | 1.2 | Multipoint QTL Mapping in Genetically Heterogeneous Animals |
| hmmer | 3.1b1 | profile hidden Markov models for protein sequence analysis |
| hyphy | 2.1+20111219 | analysis of genetic sequences using multiple techniques |
| infernal | 1.1.1 | inference of RNA secondary structural alignments |
| isacreator | 1.6.0 | GUI to import and edit ISA dataset descriptions. |
| jaligner | 1.0+dfsg | Smith-Waterman algorithm with Gotoh’s improvement |
| jalview | 2.8.0b1.dfsg | multiple alignment editor |
| jellyfish | 2.2.3 | count k-mers in DNA sequences |
| jemboss | 6.6.0+dfsg | graphical user interface to EMBOSS |
| jmotu | 1.0.6 | Clusters barcode DNA sequence data into molecular operational taxonomic units |
| jprofilegrid | 2.0.5 | Multiple sequence alignment tool that generates ProfileGrids |
| keyring | 6 | Public key package for the Bio-Linux package repository |
| khmer | 1.1 | k-mer counting, filtering and graph traversal |
| khmer-example | 1.1 | k-mer counting, filtering and graph traversal |
| last-align | 393 | genome-scale comparison of biological sequences |
| lastz | 1.02.00 | Aligns two DNA sequences, inferring appropriate parameters automatically |
| libbiojava-java | 1:1.7.1 | Java API to biological data and applications (default version) |
| libbiojava-java-demos | 1:1.7.1 | Example programs for BioJava |
| libpandaseq-sam1 | 1.2~ppa0 | Pair-end read assembler |
| libpandaseq-url0 | 2.7~ppa0 | Pair-end read assembler — URL handler |
| libpandaseq5 | 2.7~ppa0 | Pair-end read assembler |
| lucy | 1.19p | Preparation of raw DNA sequence fragments for sequence assembly |
| macs14 | 1.4.2.1 | Model-based Analysis of ChIP-Seq on short reads sequencers |
| mafft | 7.215 | Multiple alignment program for amino acid or nucleotide sequences |
| maq | 0.7.1 | maps short fixed-length polymorphic DNA sequence reads to reference sequences |
| maxd | 2.3.0 | maxd is a data warehouse and visualisation environment for genomic expression data. |
| mdust | 1:0.1+20020708 | repetitive sequence masker |
| meme | 1:4.10.0.1 | search for common motifs in DNA or protein sequences |
| mesquite | 2.74 | Software for evolutionary biology. |
| metavelvet | 1.2.02 | extension of Velvet assembler to de novo metagenomic assembly |
| microbiomeutil | 20101212+dfsg | Microbiome Analysis Utilities |
| mira-3rdparty | 20120706 | Additional useful tools to accomapany the MIRA assembler |
| mira-assembler | 4.9.5 | Whole Genome Shotgun and EST Sequence Assembler |
| mothur | 1.36.1+dfsg | sequence analysis suite for research on microbiota |
| mothur-lookup-files | 1 | .pat lookup files for Mothur |
| mothur-mpi | 1.36.1+dfsg | mpi-enabled binary for mothur |
| mrbayes-mpi | 3.2.2+dfsg | Bayesian Inference of Phylogeny – mpi version |
| msatfinder | 2.0.10 | Microsatellite Finder |
| mspcrunch | 2.5 | a BLAST post-processing filter. |
| mummer | 3.23~dfsg | Efficient sequence alignment of full genomes |
| muscle | 1:3.8.31 | Multiple alignment program of protein sequences |
| mview | 1.51 | Multiple alignment viewer for sequence database search results. |
| natefoo-add-scores | 0.1+20101006 | small helper application used by Galaxy server |
| natefoo-taxonomy | 0.1+20101102 | small taxonomy applications used by Galaxy server |
| ncbi-blast+ | 2.2.28 | next generation suite of BLAST sequence search tools |
| ncbi-blast+-legacy | 2.2.28 | NCBI Blast legacy call script |
| ncbi-seg | 0.0.20000620 | tool to mask segments of low compositional complexity in amino acid sequences |
| ncbi-tools-bin | 6.1.20120620 | NCBI libraries for biology applications (text-based utilities) |
| ncbi-tools-x11 | 6.1.20120620 | NCBI libraries for biology applications (X-based utilities) |
| njplot | 2.4 | phylogenetic tree drawing program |
| nrdb | 2 | Generates quasi-nonredundant protein and nucleotide sequence databases |
| ocount | 0.5 | Oligonucleotide frequency counter |
| oligoarray | 2.1 | Computes oligonucleotides for microarray construction |
| oligoarrayaux | 3.7 | Free software that is required for the OligoArray2.1 software. |
| omegamap | 0.5 | Detects natural selection and recombination in DNA or RNA sequences. |
| paml | 4.7 | Phylogenetic Analysis by Maximum Likelihood (PAML) |
| pandaseq | 2.7~ppa0 | Pair-end read assembler |
| pandaseq-dev | 2.7~ppa0 | Pair-end read assembler — Development tools |
| pandaseq-sam | 1.2~ppa0 | Pair-end read assembler |
| pandaseq-sam-dev | 1.2~ppa0 | Pair-end read assembler — Development tools |
| parafly | 0.0.2013.01.21 | parallel command processing using OpenMP |
| parsinsert | 1.04 | Parsimonious Insertion of unclassified sequences into phylogenetic trees |
| pass2 | 0.1+20101008 | Peak calling in ChIP data based on Poisson de-clumping |
| perm | 0.4.0 | Efficient mapping of short reads with periodic spaced seeds |
| pfaat | 1.0.034 | Sequence alignment editor designed for protein family analysis. |
| phylip | 1:3.695 | No description |
| phyml | 2:20120412 | Phylogenetic estimation using Maximum Likelihood |
| picard-tools | 1.105 | Command line tools to manipulate SAM and BAM files |
| plymouth-theme | 8.2 | Boot splash for Bio-Linux 8 |
| prank | 0.0.140110 | Probabilistic Alignment Kit for DNA, codon and amino-acid sequences |
| predictprotein | 1.0.94 | suite of protein sequence analysis tools |
| priam | 2005.07 | Generate enzyme-specific profiles for metabolic pathyway prediction |
| primer3 | 2.3.6 | Tool to design flanking oligo nucleotides for DNA amplification |
| probcons | 1.12 | PROBabilistic CONSistency-based multiple sequence alignment |
| pymol | 1.7.2.1 | Molecular Graphics System |
| qiime | 1.9.1+dfsg | Quantitative Insights Into Microbial Ecology |
| qiime-default-reference | 0.1.3 | QIIME default reference dataset |
| qtlcart | 1.17f | Map quantitative traits using a map of molecular markers. |
| r-base | 3.2.2 | GNU R statistical computation and graphics system |
| r-base-core | 3.2.2 | GNU R core of statistical computation and graphics system |
| r-base-dev | 3.2.2 | GNU R installation of auxiliary GNU R packages |
| r-bioc-affy | 1.46.1 | GNU R package “Methods for Affymetrix Oligonucleotide |
| r-bioc-affyio | 1.36.0 | GNU R package “Tools for parsing Affymetrix data files” |
| r-bioc-annotate | 1.42.0 | GNU R package “Annotation for microarrays” |
| r-bioc-annotationdbi | 1.26.0 | GNU R package “Annotation Database Interface” |
| r-bioc-biobase | 2.28.0 | GNU R package “Biobase: Base functions for Bioconductor” |
| r-bioc-biocgenerics | 0.14.0 | GNU R package “S4 generic functions for Bioconductor” |
| r-bioc-biocinstaller | 1.18.4 | GNU R package “Install/Update Bioconductor and CRAN |
| r-bioc-biocparallel | 1.2.9 | GNU R package “Bioconductor facilities for parallel |
| r-bioc-biomart | 2.18.0 | GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene) |
| r-bioc-biostrings | 2.36.4 | GNU R package “String objects representing biological |
| r-bioc-bitseq | 1.8.0 | Bioconductor package “Transcript expression inference and differential |
| r-bioc-deseq | 1.16.0 | Differential gene expression analysis based on the -ve binomial distribn. |
| r-bioc-edger | 3.6.2 | GNU R package “Empirical analysis of digital gene |
| r-bioc-genefilter | 1.46.1 | GNU R package “genefilter: methods for filtering genes |
| r-bioc-geneplotter | 1.42.0 | Graphics related functions for Bioconductor |
| r-bioc-genomeinfodb | 1.4.2 | GNU R package “Utilities for manipulating chromosome and |
| r-bioc-genomicalignments | 1.4.1 | GNU R package “Representation and manipulation of short |
| r-bioc-genomicranges | 1.20.6 | GNU R package “Representation and manipulation of genomic |
| r-bioc-hilbertvis | 1.23.0 | GNU R package to visualise long vector data |
| r-bioc-impute | 1.38.1 | GNU R package “impute: Imputation for microarray data” |
| r-bioc-iranges | 2.2.7 | GNU R package “Infrastructure for manipulating intervals |
| r-bioc-limma | 3.20.5 | GNU R package “Linear Models for Microarray Data” |
| r-bioc-multtest | 2.24.0 | GNU R package “Resampling-based multiple hypothesis |
| r-bioc-pcamethods | 1.54.0 | Bioconductor “pcaMethods: A collection of PCA methods.” |
| r-bioc-preprocesscore | 1.30.0 | GNU R package “A collection of pre-processing functions” |
| r-bioc-qvalue | 1:1.38.0 | Bioconductor package “Q-value estimation for false discovery rate control” |
| r-bioc-rsamtools | 1.20.4 | GNU R package “Binary alignment (BAM), variant call (BCF), |
| r-bioc-s4vectors | 0.6.5 | GNU R package “S4 implementation of vectors and lists” |
| r-bioc-xvector | 0.8.0 | GNU R package “Representation and manpulation of external |
| r-bioc-zlibbioc | 1.10.0 | GNU R package “An R packaged zlib-1.2.5″ |
| r-cran-abind | 1.4-0 | GNU R package “Combine multi-dimensional arrays” |
| r-cran-ade4 | 1.7-2 | GNU R package “Analysis of Ecological Data : Exploratory |
| r-cran-ape | 3.3 | GNU R package “Analyses of Phylogenetics and Evolution” |
| r-cran-aplpack | 1.3.0 | GNU R package “Another Plot PACKage: stem.leaf, bagplot, |
| r-cran-bitops | 1.0-6 | GNU R package implementing bitwise operations |
| r-cran-catools | 1.17.1 | GNU R package “Tools: moving window statistics, GIF, |
| r-cran-cluster | 2.0.3 | GNU R package for cluster analysis by Rousseeuw et al |
| r-cran-data.table | 1.9.4 | GNU R package “Extension of data.frame” |
| r-cran-dbi | 0.3.1 | GNU R package “R Database Interface” |
| r-cran-dichromat | 2.0.0 | Color schemes for dichromats |
| r-cran-digest | 0.6.8 | GNU R package “Create Cryptographic Hash Digests of R |
| r-cran-evaluate | 0.7.2 | GNU R package “Parsing and Evaluation Tools that Provide |
| r-cran-futile.logger | 1.4.1 | GNU R package “A Logging Utility for R” |
| r-cran-futile.options | 1.0.0 | GNU R package “Futile options management” |
| r-cran-gdata | 2.17.0 | GNU R package “Various R Programming Tools for Data |
| r-cran-gee | 4.13-19 | GNU R package “Generalized Estimation Equation Solver” |
| r-cran-getopt | 1.20.0 | GNU R package “C-like getopt behavior.” |
| r-cran-ggplot2 | 1.0.1 | GNU R package “An Implementation of the Grammar of |
| r-cran-gplots | 2.17.0 | GNU R package “Various R Programming Tools for Plotting |
| r-cran-gtable | 0.1.2 | GNU R package “Arrange grobs in tables.” |
| r-cran-gtools | 3.5.0 | GNU R package “Various R Programming Tools” |
| r-cran-labeling | 0.3 | GNU R package “Axis Labeling” |
| r-cran-lambda.r | 1.1.7 | GNU R package “Modeling Data with Functional Programming” |
| r-cran-lattice | 0.20-29 | GNU R package “Lattice Graphics” |
| r-cran-leaps | 2.9 | GNU R package “regression subset selection” |
| r-cran-lme4 | 1.1-9 | GNU R package for linear mixed effects model fitting |
| r-cran-locfit | 1.5-9.1 | Local Regression, Likelihood and Density Estimation. |
| r-cran-matrix | 1.2-2 | GNU R package of classes for dense and sparse matrices |
| r-cran-matrixstats | 0.10.0 | R package “Methods that apply to rows and columns of a matrix” |
| r-cran-munsell | 0.4.2 | GNU R package “Munsell colour system” |
| r-cran-nlme | 3.1.122 | GNU R package for (non-)linear mixed effects models |
| r-cran-optparse | 1.2.0 | GNU R package “Command line option parser.” |
| r-cran-permute | 0.8-4 | GNU R package “Functions for Generating Restricted |
| r-cran-plotrix | 3.5-7 | GNU R package “Various plotting functions” |
| r-cran-plyr | 1.8.3 | GNU R package “Tools for Splitting, Applying and Combining |
| r-cran-prettyr | 2.0-8 | GNU R package “Pretty descriptive stats.” |
| r-cran-propcis | 0.2-5 | GNU R package “PropCIs: Various confidence interval methods for proportions” |
| r-cran-proto | 0.3-10 | GNU R package “Prototype object-based programming” |
| r-cran-r.methodss3 | 1.6.1 | GNU R package “Utility function for defining S3 methods” |
| r-cran-rapidr | 0.1.1 | GNU R package “RAPIDR: Reliable Accurate Prenatal non-Invasive Diagnosis.” |
| r-cran-rcolorbrewer | 1.0-5 | GNU R package providing suitable color palettes |
| r-cran-rcpp | 0.12.1 | GNU R package “Seamless R and C++ Integration” |
| r-cran-rcurl | 1.95-4.7 | GNU R package “General Network (HTTP/FTP/…) Client |
| r-cran-relimp | 1.0-4 | GNU R package “Relative Contribution of Effects in a |
| r-cran-reshape2 | 1.4.1 | GNU R package “Flexibly Reshape Data: A Reboot of the |
| r-cran-rggobi | 2.1.20 | GNU R package for the GGobi data visualization system |
| r-cran-rgl | 0.95.1247 | GNU R package for three-dimensional visualisation using OpenGL |
| r-cran-rgtk2 | 2.20.31 | GNU R binding for Gtk2 |
| r-cran-rmpi | 0.6-5 | GNU R package interfacing MPI libraries for distributed computing |
| r-cran-rserve | 1.7-3 | GNU R Rserve tcp/ip server and sample clients |
| r-cran-rsqlite | 1.0.0 | GNU R package “SQLite Interface for R” |
| r-cran-rwave | 2.4 | GNU R package “Time-Frequency Analysis of 1-D Signals” |
| r-cran-samr | 2.0 | GNU R package “SAM: Significance Analysis of Microarrays” |
| r-cran-scales | 0.3.0 | GNU R package “Scale Functions for Visualization” |
| r-cran-scatterplot3d | 0.3-36 | GNU R package “3D Scatter Plot” |
| r-cran-snowfall | 1.84-6 | GNU R package “Easier cluster computing (based on snow).” |
| r-cran-sp | 1:1.1-0 | GNU R package “Classes and Methods for Spatial Data” |
| r-cran-stringr | 1.0.0 | GNU R package “Simple, Consistent Wrappers for Common |
| r-cran-tcltk2 | 1.2-9 | GNU R package “Tcl/Tk Additions” |
| r-cran-testthat | 0.9.1 | GNU R package “Testthat code. Tools to make testing fun |
| r-cran-vegan | 2.3-0 | GNU R package “Community Ecology Package” |
| r-cran-waveslim | 1.7.5 | GNU R package “Basic wavelet routines for one-, two- and |
| r-cran-wavethresh | 4.6.6 | GNU R package “Wavelets statistics and transforms.” |
| r-cran-xml | 3.98-1.3 | GNU R package “Tools for Parsing and Generating XML Within |
| r-cran-xtable | 1:1.7-3 | GNU R coerce data to LaTeX and HTML tables |
| r-mathlib | 3.2.2 | GNU R standalone mathematics library |
| r-recommended | 3.2.2 | GNU R collection of recommended packages [metapackage] |
| rasmol | 2.7.5.2 | Visualize biological macromolecules |
| raxml | 8.0.26 | Randomized Axelerated Maximum Likelihood of phylogenetic trees |
| ray | 2.3.1 | parallel de novo genome assemblies of next-gen sequencing data |
| ray-extra | 2.3.1 | Scripts and XSL sheets for post-processing for ray de novo assembler |
| rbs-finder | 1.0 | A program to find Ribosomal binding sites. |
| rdp-classifier | 2.10.2+dfsg | taxonomic assignment from next generation sequencing |
| readseq | 1 | Conversion between sequence formats |
| rsem | 1.2.22+dfsg | RNA-Seq by Expectation-Maximization |
| sampledata | 20041011 | Sample data for Bio-Linux packages |
| samtools | 0.1.19 | processing sequence alignments in SAM and BAM formats |
| scythe | 0.993 | Bayesian adapter trimmer for nextgen sequence reads |
| seaview | 1:4.4.2 | No description |
| seqprep | 1.1 | tool for stripping adaptors and/or merging paired reads with overlap |
| shared | 1.1 | Some shared files used by Bio-Linux |
| sickle | 1.33 | windowed adaptive trimming tool for FASTQ files using quality |
| sift | 4.0.3b | predicts if a substitution in a protein has a phenotypic effect |
| sortmerna | 2.0 | tool for filtering, mapping and OTU-picking NGS reads |
| splitstree | 4.12.6 | Analysis and visualisation tool for distance data from biological sequences |
| sputnik-mononucleotide | 0.1+20101005 | Searches DNA sequence files in FASTA format for microsatellite repeats |
| squint | 1.02 | Java-based multiple alignment program and editor |
| ssake | 3.8.1 | genomics application for assembling millions of very short DNA sequences |
| stacks | 1.34 | pipeline for building loci from short-read sequences |
| stacks-web | 1.34 | web interface for displaying loci from short-read sequences |
| staden | 2.0.0b10 | DNA sequence assembly (Gap4/Gap5), editing and analysis tools |
| staden-common | 2.0.0b10 | Architecture independent files for Staden |
| stars | 1.2a | STARS is an alternative interface to Staden. |
| sumatra | 1.0.01 | fast and exact comparison and clustering of sequences |
| swarm | 1.2.20 | robust and fast clustering method for amplicon-based studies |
| t-coffee | 10.00.r1613 | Multiple Sequence Alignment |
| tablet | 1.14.04.10 | Graphical viewer for next gen sequence assemblies and alignments |
| taxinspector | 1.0b3 | Browser for entries in the NCBI taxonomy database |
| tetra | 1.0b3 | tetranucleotide frequency calculator with GUI |
| themes-v7 | 7.0 | Graphics, icons, wallpaper and desktop settings for Bio-Linux 7 |
| themes-v8 | 8.0 | Graphics, icons, wallpaper and desktop settings for Bio-Linux 8 |
| tophat | 2.1.0 | fast splice junction mapper for RNA-Seq reads |
| trace2dbest | 3.14 | Processes trace files into dbEST submissions |
| transdecoder | 2.0.1+dfsg | find coding regions within transcripts |
| transterm-hp | 2.07 | Transterm finds rho-independent transcription terminators in bacterial genomes. |
| transtermhp | 2.09 | find rho-independent transcription terminators in bacterial genomes |
| tree-puzzle | 5.2 | Reconstruction of phylogenetic trees by maximum likelihood |
| tree-puzzle-doc | 5.2 | Reconstruction of phylogenetic trees by maximum likelihood |
| treeviewx | 0.5.1+20100823 | Displays and prints phylogenetic trees |
| trinityrnaseq | 2.0.6+dfsg | RNA-Seq De novo Assembly |
| trinityrnaseq-sampledata | 2.0.6+dfsg | RNA-Seq De novo Assembly |
| trnascan | 1.23 | tRNAscan-SE searches for tRNA genes in genomic sequences. |
| trnascan-se | 1.3.1 | search for tRNA genes in genomic sequences |
| tutorials | 1 | Tutorials and documentation for Bio-Linux users. |
| ugene | 1.18.0+repack | integrated bioinformatics toolkit |
| unity-lens | 0.2 | unity lens for Bio-Linux |
| usb-maker | 8.2 | Script to generate Bio-Linux live memory sticks. |
| velvet | 1.2.10+dfsg | Nucleic acid sequence assembler for very short reads |
| velvet-example | 1.2.10+dfsg | Example data for the Velvet sequence assembler |
| velvet-long | 1.2.10+dfsg | Nucleic acid sequence assembler for very short reads, long version |
| velvetoptimiser | 2.2.5 | Automatically optimise Velvet do novo assembly parameters |
| vsearch | 1.1.1.nodata | tool for processing metagenomic sequences |
| weblogo | 3.3 | create sequence logos from biological sequence alignments |
| wise | 2.4.1 | comparison of biopolymers, commonly DNA and protein sequences |
| xcut | 1.4.2 | A re-write of the GNU cut command with many new features. |
| zsh | 1 | Z-Shell wrapper package for Bio-Linux. |
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