biolinux操作系统简介
biolinux操作系统简介
简介
Bio-linux由NERC Environmental Bioinformatics Centre开发并维护，详细内容请访问bio-linux主页。 http://environmentalomics.org/bio-linux/
如果你想了解或引用biolinux，请查看或引用关于biolinux的发表在Nature Biotechnology（自然生物技术）上的文章Open Software for biologists: from famine to feast。
功能
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。
最新发生版为Bio-Linux8.0, 基于Ubuntu 12.04 x64版本，发布于2014年7月，安装程序大小为2G，安装需要至少15G硬盘空间。
内部集成了500多个生物信息学人员常用的软件或包，也可自己将biolinux软件源加入Ubuntu软件列表中，利用Ubuntu的apt-get安装这些软件包。常用软件列表见表1，附中文简介。
表1. Bio-linux8集成主要生物信息学软件简介
| act | 13.2-1 | A DNA sequence comparison viewer based on Artemis | 基于Artemis的DN序列可视化比较工具 |
| ampliconnoise | 1bl-0 | Programs for the removal of noise from 454 sequenced PCR amplicons | 去除454测序PCR扩增噪音序列 |
| arb | 1:1bl1-3 | Graphical sequence and data analysis tools. | 图形化序列分析工具 |
| archaeopteryx | 0.972.beta9M-3 | A phylogenetic tree viewer and editor | 进化树查看编辑器 |
| artemis | 13.2-6 | Free genome viewer and annotation tool | 免费的本地基因组浏览器 |
| assembly-conversion-tools | 0.01-10 | Conversion tools for handling 454 assemblies. | 454序列拼接转换工具 |
| backups | 0.3-6 | Bio-Linux 5/6 backup utilities. | biolinx5/6旧版本支持组件 |
| base-directories | 1.0-37 | Essential Bio-Linux configuration files. | 生物信息平台重要配置文件 |
| big-blast | 1.0.3-4 | The big-blast script for annotation of long sequences | 注释长序列的big-blast脚本 |
| biocode | 2.3.3-2 | Biocode plugin for Geneious workbench | Geneious workbech的Biocode插件 |
| biojava | 1.7.1-3 | Open-source Java framework for processing biological data. | Java生物信息相关包 |
| blast | 1:1bl-7 | Rapid searching of nucleotide and protein databases. | 最著名的序列比对软件 |
| blast+ | 1:1bl1 | Blast+ contains new builds of the popular blast family of programs from the NCBI. | blast的衍生版 |
| bldp-files | 1.1-96 | Documentation for bioinformatics software on Bio-Linux. | 平台软件说明文档 |
| blixem | 3.1.1-3 | Interactive browser for viewing pairwise Blast results. | 可查看blast结果的交互式浏览器 |
| cap3 | 20080520-1 | A base calling system | base calling系统，是将测序的图片结果转换成序列的过程 *我以前用过cap3的软件是做序列拼接的，不知这是标错了，还是另一个软件 |
| catchall | 3.0.1-1 | Analyze data about microbial species abundance | 分析微生物特种丰度数据 |
| cd-hit | 2009-1020-1 | a suite of programs designed to quickly group sequences | 序列聚类分组工具箱 |
| cdbfasta | 1:20100722bl-3 | FASTA file indexing and retrieval tools | fasta格式序列文件索引和检索工具 |
| chimeraslayer | 1:20100429bl-4 | chimeric detection utility for 16S rRNA | 16S rRNA混合结果检测分析工具 |
| clcsequenceviewer | 6.4-1 | CLC Free Sequence Viewer | CLC序列查看器 |
| cloudbl-desktop | 1.4 | Adds useful links to the remote desktop for Cloud BL | 云服务 |
| clustal | 1:1bl-7 | Installs clustalw and clustalx for multiple sequence and profile alignments. | 多序列比对 |
| cytoscape | 1:2.7.0-8 | Platform for visualizing complex-networks and integrating these with attribute data | 著名基因网络分析平台，复杂调控网络、GO分析 |
| dendroscope | 1.4.0-5 | Interactive viewer for large phylogenetic trees. | 进化树查看器 |
| denoiser | 1:0.851-9 | Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distribution | 高通量测序扩增噪音去除 |
| dialign | 1:1bl-2 | Segment-based multiple sequence alignment DIALIGN2 is a command line tool to perform multiple alignment of protein or DNA sequences. It constructs alignments from gapfree pairs of similar segments of the sequences. This scoring scheme for alignments is the basic difference between DIALIGN and other global or local alignment methods. Note that DIALIGN does not employ any kind of gap penalty. It has been published by Morgenstern B. in Bioinformatics. 1999 Mar;15(3):211-8. | 多序列比对 |
| dotter | 3.1-1 | Graphical dotplot program for detailed comparison of two sequences | 两序列dotplot图比较 |
| dust | 2bl1-2 | Repetitive sequence masker | 重复序列识别 |
| embassy-domainatrix | 0.1.0+20100115-1 | Extra EMBOSS commands to handle domain classification file | EMBOSS工具集：结构域分类 |
| embassy-domalign | 0.1.0+20100115-1 | Extra EMBOSS commands for protein domain alignment | EMBOSS工具集：结构域比对 |
| embassy-domsearch | 0.1.0++20100115-1 | Extra EMBOSS commands to search for protein domains | EMBOSS工具集：结构域检索 |
| embassy-phylip | 3.69-1 | EMBOSS conversions of the programs in the phylip package | EMBOSS工具集：进化分析 |
| emboss | 1:1bl1-1 | extensive set of tools for bioinformatics and biological database management | EMBOSS工具集：数据库管理 |
| emboss-data | 6.3.1-3 | data files for the EMBOSS package | EMBOSS工具集：数据文件 |
| emboss-doc | 6.3.1-3 | documentation for EMBOSS | EMBOSS工具集：说明文档 |
| emboss-lib | 6.3.1-3 | EMBOSS Libraries | EMBOSS工具集：库文件 |
| emboss-test | 6.3.1-3 | test files for the EMBOSS package | EMBOSS工具集：测试文件 |
| estscan | 2.1-12 | detects coding regions of DNA sequences. | 检测DNA编码区 |
| exchanger | 1.0-5 | lets you store, annotate and share files via an omixed server | 数据注释共享服务 |
| fasta | 36t2d5-1 | Collection of programs for searching DNA and protein databases. | 类似于blast的序列比对 |
| fastdnaml | 1:1bl-2 | estimates maximum likelihood phylogenetic trees from nucleotide sequences | 进化树分析 |
| fastqc | 0.10.1-2 | A quality control application for high throughput sequence data | 高通量测序质量控制软件 |
| fasttree | 2.1.3-1 | Infers approximately-maximum-likelihood phylogenetic trees | 进化树分析 |
| forester | 1.92-10 | ATV (A Tree Viewer) is a Java tool for the visualization of annotated phylogenetic trees. | 进化树可视化 |
| gap2caf | 0.20100408-2 | Handles conversion of gap format assemblies to caf format. | 格式转换gap为caf |
| geneious | 5.5.7-3 | Geneious Basic workbench from Biomatters | 综合分析平台 |
| geneious-genbanksubmit | 1.3.0-1 | GenBank submission for Geneious workbench | 序列提交工具 |
| genquery | 2.2.4-3 | GenQuery is a set of Perl libraries for managing SQL query templates and making web-based query forms. | Perl包，数据库检索 |
| glimmer3 | 3.02-1 | System for finding genes in microbial DNA. | 微生物基因鉴定 |
| handlebar | 2.2.2-7 | Handlebar is a database for storing data about barcodes and acessing the data via a web front-end. | 数据管理数据库 |
| happy | 1.2-2 | Multipoint QTL Mapping in Genetically Heterogeneous Animals | 多点QTL作图 |
| hmmer | 1:1bl-1 | HMM methods for searching databases for multiple sequence alignments | 隐马方式的多序列比对 |
| isacreator | 1.6.0-1 | GUI to import and edit ISA dataset descriptions. | ISA数据描述导入与编辑 |
| jalview | 1:2.7.0-2 | a Java multiple alignment editor | Java多比对编辑器 |
| jemboss | 6.3bl1-8 | graphical user interface to EMBOSS | EMBOSS图形界面 |
| jmotu | 1.0.6-2 | Clusters barcode DNA sequence data into molecular operational taxonomic units | DNA序列聚类 |
| jprofilegrid | 1:1bl-2 | Multiple sequence alignment tool that generates ProfileGrids | 多序列比对 |
| keyring | 5 | Public key package for the Bio-Linux package repository | Bio-linux软件包 |
| libajax6 | 6.3.1-3 | EMBOSS library for commands | EMBOSS库 |
| libajax6-dev | 6.3.1-3 | development files for libajax | libajax开发文件 |
| libnucleus6 | 6.3.1-3 | EMBOSS library for molecular sequence analysis | EMBOSS库：分子序列分析 |
| libnucleus6-dev | 6.3.1-3 | development files for libnucleus | libnucleus开发文件 |
| lucy | 1:1bl-1 | Preparation of raw DNA sequence fragments for sequence assembly. | 原始DNA序列处理用于组装 |
| mcl | 1:1bl-2 | Tools for clustering protein groups in to protein families. | 蛋白家族聚类 |
| mesquite | 2.74-3 | Software for evolutionary biology. | 进化生物学 |
| mira | 1:1bl-2 | Assembly and editing of nucleotide sequences, including 454 and Solexa support | 组装和编辑序列，支持NGS新一代测序 |
| mira-3rd-party | 1:1bl-1 | Provides useful script for sequence handling | 序列处理 |
| mothur | 2bl-5 | This is a wrapper package for mothur | mothus相关包 |
| mrbayes | 1:2bl-3 | Bayesian estimation of phylogeny | 基于贝叶斯估计的系统发育分析 |
| mrbayes-multi | 3.1.2-4 | Multiprocessor version of MrBayes | 多线程版的MrBayes |
| msatfinder | 2.0.10-1 | Microsatellite Finder | 鉴定微卫星 |
| mspcrunch | 2.5-1 | a BLAST post-processing filter. | blast结果分析 |
| mummer | 1:1bl-1 | a system for rapidly aligning entire genomes. | 序列比对 |
| muscle | 1:1bl-2 | Bio-Linux wrapper for the Debian Med muscle package | med muscle包 |
| mview | 1.51-3 | Multiple alignment viewer for sequence database search results. | 序列检索结果的多序列比对浏览器 |
| ncbi-tools-x11 | 1:1bl-3 | NCBI libraries for biology applications (X-based utilities) | NCBI库 |
| njplot | 1:1bl-2 | Phylogenetic tree drawing program. | 系统发育树 |
| nrdb | 2-1 | Generates quasi-nonredundant protein and nucleotide sequence databases. | 产生类似非冗余蛋白和核酸序列数据库 |
| ocount | 0.5-1 | Oligonucleotide frequency counter | 寡核苷酸频率统计 |
| oligoarray | 2.1-11 | Computes oligonucleotides for microarray construction | 芯片设计 |
| oligoarrayaux | 3.7-1 | Free software that is required for the OligoArray2.1 software. | 芯片设计升级版 |
| omegamap | 0.5-1 | Detects natural selection and recombination in DNA or RNA sequences. | 检测DNA/RNA序列自然选择和重组 |
| paml | 1:1bl1 | Phylogenetic analysis for DNA/protein sequences using max. likelihood | 最大似然数法的蛋白/核酸系统发生分析 |
| pfaat | 1.0.034-7 | Sequence alignment editor designed for protein family analysis. | 蛋白家族的多序列比对分析 |
| phylip | 1:1bl-2 | Tool for inferring phylogenies. | 系统发生分析 |
| phyml | 1:1bl-1 | Phylogeny software based on the maximum-likelihood principle. | 最大似然数法的系统发生分析 |
| plymouth-theme | 7.0 | Boot splash for Bio-Linux 7 | 开机画面程序 |
| prank | 1:1bl1-2 | Multiple alignment software. | 多序列比对软件 |
| prevent-upgrade | 0.2 | Stop Bio-Linux from upgrading on release of 12.04 LTS | 防自动升级程序(Ubuntu各版本兼容性差异很大，升级会导致很多软件出错) |
| priam | 2005.07-5 | Generate enzyme-specific profiles for metabolic pathyway prediction | 产生酶特异性谱用于代谢通路预测 |
| primer3 | 1:1bl-1 | Primer3 picks primers for PCR reactions. | PCR引物设计 |
| python-cogent | 1:1.4.1bl-1 | Python-cogent, or PyCogent, is a python library for genomic biology. | python基因组生物学包 |
| qiime | 2:1bl-8 | Quantitative insights into microbial ecology | 定量微生物生态 |
| qtlcart | 1.17f-2 | Map quantitative traits using a map of molecular markers. | 基于分子标记的数量性状定位 |
| rasmol | 1:1bl-1 | Molecular genetics visualisation tool. | 分子遗传可视化工具 |
| rbs-finder | 1.0-4 | A program to find Ribosomal binding sites. | rRNA结合位点预测 |
| rdp-classifier | 2:1bl1-1 | A niave Bayesian classifier for 16S rRNA sequences. | 基于贝叶斯算法 的16S rRNA分类 |
| readseq | 1:1bl-3 | Read and reformat biosequences | 生物序列格式转换 |
| sampledata | 20041011-10 | Sample data for Bio-Linux packages | 平台测序数据集 |
| samtools | 1:1bl-3 | processing sequence alignments in SAM and BAM formats | SAM/BAM文件转换分析 |
| seaview | 1:1bl1-1 | Multiple sequence alignment editor | 多序列比对编辑 |
| sequin | 1:1bl-0 | Transitional package that provides bio-linux-ncbi-tools-x11 | 序列提交NCBI客户端 |
| shared | 1.1-2 | Some shared files used by Bio-Linux | 共享库 |
| splitstree | 4.12.6-2 | Analysis and visualisation tool for distance data from biological sequences | 远源序列分析 |
| squint | 1.02-4 | Java-based multiple alignment program and editor | 多序列比对java版 |
| staden | 2006.1.7.0+1.11.6-8 | A suite of tools for sequence analysis. | 序列分析工具集 |
| stars | 1.2a-12 | STARS is an alternative interface to Staden. | staden的用户界面 |
| t-coffee | 1:1bl-3 | Multiple Sequence Alignment | 多序列比对 |
| tablet | 1.12.03.26-1 | Graphical viewer for next gen sequence assemblies and alignments | 高通量测序比对结果可视化程序，同Gbrowser |
| taxinspector | 1.0b3-12 | Browser for entries in the NCBI taxonomy database | 生物分类数据 |
| tetra | 1.0b3-1 | tetranucleotide frequency calculator with GUI | 图型界面的核酸频率统计 |
| themes | 6.1 | Graphics, icons, wallpaper and a GDM theme for Bio-Linux 6. | 主题v6 |
| themes-v5 | 1.2 | Graphics, icons, KDE splash screen and a GDM theme for Bio-Linux 5. | 主题v5 |
| themes-v7 | 7.0-12 | Graphics, icons, wallpaper and desktop settings for Bio-Linux 7 | 主题v7 |
| transterm-hp | 1:1bl1-1 | finds rho-independent transcription terminators in bacterial genomes | 在细胞基因组中，查找rho因子不依赖的转录终止子 |
| tree-puzzle | 1:1bl-1 | pylogenetic tree reconstruction from molecular sequence | 基于分子序列的系统发生树构建 |
| treeview | 1:1bl-1 | A simple program for displaying phylogenies. | 系统发生/进化树显示 |
| trnascan | 1:1bl1-1 | searches for tRNA genes in genomic sequences. | 基因组tRNA预测 |
| tutorials | 1-23 | Tutorials and documentation for Bio-Linux users. | 帮助文档 |
| unity-lens | 0.2 | unity lens for Bio-Linux | 搜索滤镜 |
| usb-maker | 7.0-1 | Script to generate Bio-Linux live memory sticks. | USB版系统定制程序 |
| wise2 | 1:1bl1-2 | Tool for comparison of biopolymers, DNA, and protein sequence. | 比较生物序列聚合物 |
| xcut | 1.4-3 | A re-write of the GNU cut command with many new features. | cut改进版 |
| zsh | 1-18 | Z-Shell wrapper package for Bio-Linux. | Z-shell |
biolinux 官方网站：http://nebc.nerc.ac.uk
- 发表于 2019-10-15 13:29
- 阅读 ( 6155 )
- 分类：linux
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