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這篇文章主要介紹“biolinux操作系統(tǒng)有哪些功能”的相關(guān)知識(shí)，小編通過(guò)實(shí)際案例向大家展示操作過(guò)程，操作方法簡(jiǎn)單快捷，實(shí)用性強(qiáng)，希望這篇“biolinux操作系統(tǒng)有哪些功能”文章能幫助大家解決問(wèn)題。
Bio-linux由NERC Environmental Bioinformatics Centre開(kāi)發(fā)并維護(hù)，詳細(xì)內(nèi)容請(qǐng)?jiān)L問(wèn)bio-linux主頁(yè)。 http://environmentalomics.org/bio-linux/
如果你想了解或引用biolinux，請(qǐng)查看或引用關(guān)于biolinux的發(fā)表在Nature Biotechnology（自然生物技術(shù)）上的文章Open Software for biologists: from famine to feast。
Bio-Linux是功能齊全的、強(qiáng)大的、可定制的、易于維護(hù)的生物分析工作站。Bio-Linux基于Ubuntu提供500多個(gè)生物分析程序，由一個(gè)圖形化的菜單進(jìn)行管理，能方便地訪(fǎng)問(wèn)到其生物分析文檔系統(tǒng)及對(duì)測(cè)試程序有用的樣本數(shù)據(jù)。用于處理新型序列數(shù)據(jù)類(lèi)型的Bio-Linux軟件包可額外安裝。
最新發(fā)生版為Bio-Linux8.0, 基于Ubuntu 12.04 x64版本，發(fā)布于2014年7月，安裝程序大小為2G，安裝需要至少15G硬盤(pán)空間。
內(nèi)部集成了500多個(gè)生物信息學(xué)人員常用的軟件或包，也可自己將biolinux軟件源加入U(xiǎn)buntu軟件列表中，利用Ubuntu的apt-get安裝這些軟件包。常用軟件列表見(jiàn)表1，附中文簡(jiǎn)介。
表1. Bio-linux8集成主要生物信息學(xué)軟件簡(jiǎn)介
| act | 13.2-1 | A DNA sequence comparison viewer based on Artemis | 基于Artemis的DN序列可視化比較工具 |
| ampliconnoise | 1bl-0 | Programs for the removal of noise from 454 sequenced PCR amplicons | 去除454測(cè)序PCR擴(kuò)增噪音序列 |
| arb | 1:1bl1-3 | Graphical sequence and data analysis tools. | 圖形化序列分析工具 |
| archaeopteryx | 0.972.beta9M-3 | A phylogenetic tree viewer and editor | 進(jìn)化樹(shù)查看編輯器 |
| artemis | 13.2-6 | Free genome viewer and annotation tool | 免費(fèi)的本地基因組瀏覽器 |
| assembly-conversion-tools | 0.01-10 | Conversion tools for handling 454 assemblies. | 454序列拼接轉(zhuǎn)換工具 |
| backups | 0.3-6 | Bio-Linux 5/6 backup utilities. | biolinx5/6舊版本支持組件 |
| base-directories | 1.0-37 | Essential Bio-Linux configuration files. | 生物信息平臺(tái)重要配置文件 |
| big-blast | 1.0.3-4 | The big-blast script for annotation of long sequences | 注釋長(zhǎng)序列的big-blast腳本 |
| 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生物信息相關(guān)包 |
| blast | 1:1bl-7 | Rapid searching of nucleotide and protein databases. | 最著名的序列比對(duì)軟件 |
| 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. | 平臺(tái)軟件說(shuō)明文檔 |
| blixem | 3.1.1-3 | Interactive browser for viewing pairwise Blast results. | 可查看blast結(jié)果的交互式瀏覽器 |
| cap3 | 20080520-1 | A base calling system | base calling系統(tǒng)，是將測(cè)序的圖片結(jié)果轉(zhuǎn)換成序列的過(guò)程 *我以前用過(guò)cap3的軟件是做序列拼接的，不知這是標(biāo)錯(cuò)了，還是另一個(gè)軟件 |
| catchall | 3.0.1-1 | Analyze data about microbial species abundance | 分析微生物特種豐度數(shù)據(jù) |
| cd-hit | 2009-1020-1 | a suite of programs designed to quickly group sequences | 序列聚類(lèi)分組工具箱 |
| cdbfasta | 1:20100722bl-3 | FASTA file indexing and retrieval tools | fasta格式序列文件索引和檢索工具 |
| chimeraslayer | 1:20100429bl-4 | chimeric detection utility for 16S rRNA | 16S rRNA混合結(jié)果檢測(cè)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 | 云服務(wù) |
| clustal | 1:1bl-7 | Installs clustalw and clustalx for multiple sequence and profile alignments. | 多序列比對(duì) |
| cytoscape | 1:2.7.0-8 | Platform for visualizing complex-networks and integrating these with attribute data | 著名基因網(wǎng)絡(luò)分析平臺(tái)，復(fù)雜調(diào)控網(wǎng)絡(luò)、GO分析 |
| dendroscope | 1.4.0-5 | Interactive viewer for large phylogenetic trees. | 進(jìn)化樹(shù)查看器 |
| denoiser | 1:0.851-9 | Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distribution | 高通量測(cè)序擴(kuò)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. | 多序列比對(duì) |
| dotter | 3.1-1 | Graphical dotplot program for detailed comparison of two sequences | 兩序列dotplot圖比較 |
| dust | 2bl1-2 | Repetitive sequence masker | 重復(fù)序列識(shí)別 |
| embassy-domainatrix | 0.1.0+20100115-1 | Extra EMBOSS commands to handle domain classification file | EMBOSS工具集：結(jié)構(gòu)域分類(lèi) |
| embassy-domalign | 0.1.0+20100115-1 | Extra EMBOSS commands for protein domain alignment | EMBOSS工具集：結(jié)構(gòu)域比對(duì) |
| embassy-domsearch | 0.1.0++20100115-1 | Extra EMBOSS commands to search for protein domains | EMBOSS工具集：結(jié)構(gòu)域檢索 |
| embassy-phylip | 3.69-1 | EMBOSS conversions of the programs in the phylip package | EMBOSS工具集：進(jìn)化分析 |
| emboss | 1:1bl1-1 | extensive set of tools for bioinformatics and biological database management | EMBOSS工具集：數(shù)據(jù)庫(kù)管理 |
| emboss-data | 6.3.1-3 | data files for the EMBOSS package | EMBOSS工具集：數(shù)據(jù)文件 |
| emboss-doc | 6.3.1-3 | documentation for EMBOSS | EMBOSS工具集：說(shuō)明文檔 |
| emboss-lib | 6.3.1-3 | EMBOSS Libraries | EMBOSS工具集：庫(kù)文件 |
| emboss-test | 6.3.1-3 | test files for the EMBOSS package | EMBOSS工具集：測(cè)試文件 |
| estscan | 2.1-12 | detects coding regions of DNA sequences. | 檢測(cè)DNA編碼區(qū) |
| exchanger | 1.0-5 | lets you store, annotate and share files via an omixed server | 數(shù)據(jù)注釋共享服務(wù) |
| fasta | 36t2d5-1 | Collection of programs for searching DNA and protein databases. | 類(lèi)似于blast的序列比對(duì) |
| fastdnaml | 1:1bl-2 | estimates maximum likelihood phylogenetic trees from nucleotide sequences | 進(jìn)化樹(shù)分析 |
| fastqc | 0.10.1-2 | A quality control application for high throughput sequence data | 高通量測(cè)序質(zhì)量控制軟件 |
| fasttree | 2.1.3-1 | Infers approximately-maximum-likelihood phylogenetic trees | 進(jìn)化樹(shù)分析 |
| forester | 1.92-10 | ATV (A Tree Viewer) is a Java tool for the visualization of annotated phylogenetic trees. | 進(jìn)化樹(shù)可視化 |
| gap2caf | 0.20100408-2 | Handles conversion of gap format assemblies to caf format. | 格式轉(zhuǎn)換gap為caf |
| geneious | 5.5.7-3 | Geneious Basic workbench from Biomatters | 綜合分析平臺(tái) |
| 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，數(shù)據(jù)庫(kù)檢索 |
| glimmer3 | 3.02-1 | System for finding genes in microbial DNA. | 微生物基因鑒定 |
| handlebar | 2.2.2-7 | Handlebar is a database for storing data about barcodes and acessing the data via a web front-end. | 數(shù)據(jù)管理數(shù)據(jù)庫(kù) |
| happy | 1.2-2 | Multipoint QTL Mapping in Genetically Heterogeneous Animals | 多點(diǎn)QTL作圖 |
| hmmer | 1:1bl-1 | HMM methods for searching databases for multiple sequence alignments | 隱馬方式的多序列比對(duì) |
| isacreator | 1.6.0-1 | GUI to import and edit ISA dataset descriptions. | ISA數(shù)據(jù)描述導(dǎo)入與編輯 |
| jalview | 1:2.7.0-2 | a Java multiple alignment editor | Java多比對(duì)編輯器 |
| jemboss | 6.3bl1-8 | graphical user interface to EMBOSS | EMBOSS圖形界面 |
| jmotu | 1.0.6-2 | Clusters barcode DNA sequence data into molecular operational taxonomic units | DNA序列聚類(lèi) |
| jprofilegrid | 1:1bl-2 | Multiple sequence alignment tool that generates ProfileGrids | 多序列比對(duì) |
| keyring | 5 | Public key package for the Bio-Linux package repository | Bio-linux軟件包 |
| libajax6 | 6.3.1-3 | EMBOSS library for commands | EMBOSS庫(kù) |
| libajax6-dev | 6.3.1-3 | development files for libajax | libajax開(kāi)發(fā)文件 |
| libnucleus6 | 6.3.1-3 | EMBOSS library for molecular sequence analysis | EMBOSS庫(kù)：分子序列分析 |
| libnucleus6-dev | 6.3.1-3 | development files for libnucleus | libnucleus開(kāi)發(fā)文件 |
| lucy | 1:1bl-1 | Preparation of raw DNA sequence fragments for sequence assembly. | 原始DNA序列處理用于組裝 |
| mcl | 1:1bl-2 | Tools for clustering protein groups in to protein families. | 蛋白家族聚類(lèi) |
| mesquite | 2.74-3 | Software for evolutionary biology. | 進(jìn)化生物學(xué) |
| mira | 1:1bl-2 | Assembly and editing of nucleotide sequences, including 454 and Solexa support | 組裝和編輯序列，支持NGS新一代測(cè)序 |
| mira-3rd-party | 1:1bl-1 | Provides useful script for sequence handling | 序列處理 |
| mothur | 2bl-5 | This is a wrapper package for mothur | mothus相關(guān)包 |
| mrbayes | 1:2bl-3 | Bayesian estimation of phylogeny | 基于貝葉斯估計(jì)的系統(tǒng)發(fā)育分析 |
| mrbayes-multi | 3.1.2-4 | Multiprocessor version of MrBayes | 多線(xiàn)程版的MrBayes |
| msatfinder | 2.0.10-1 | Microsatellite Finder | 鑒定微衛(wèi)星 |
| mspcrunch | 2.5-1 | a BLAST post-processing filter. | blast結(jié)果分析 |
| mummer | 1:1bl-1 | a system for rapidly aligning entire genomes. | 序列比對(duì) |
| 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. | 序列檢索結(jié)果的多序列比對(duì)瀏覽器 |
| ncbi-tools-x11 | 1:1bl-3 | NCBI libraries for biology applications (X-based utilities) | NCBI庫(kù) |
| njplot | 1:1bl-2 | Phylogenetic tree drawing program. | 系統(tǒng)發(fā)育樹(shù) |
| nrdb | 2-1 | Generates quasi-nonredundant protein and nucleotide sequence databases. | 產(chǎn)生類(lèi)似非冗余蛋白和核酸序列數(shù)據(jù)庫(kù) |
| ocount | 0.5-1 | Oligonucleotide frequency counter | 寡核苷酸頻率統(tǒng)計(jì) |
| oligoarray | 2.1-11 | Computes oligonucleotides for microarray construction | 芯片設(shè)計(jì) |
| oligoarrayaux | 3.7-1 | Free software that is required for the OligoArray2.1 software. | 芯片設(shè)計(jì)升級(jí)版 |
| omegamap | 0.5-1 | Detects natural selection and recombination in DNA or RNA sequences. | 檢測(cè)DNA/RNA序列自然選擇和重組 |
| paml | 1:1bl1 | Phylogenetic analysis for DNA/protein sequences using max. likelihood | 最大似然數(shù)法的蛋白/核酸系統(tǒng)發(fā)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對(duì)分析 |
| phylip | 1:1bl-2 | Tool for inferring phylogenies. | 系統(tǒng)發(fā)生分析 |
| phyml | 1:1bl-1 | Phylogeny software based on the maximum-likelihood principle. | 最大似然數(shù)法的系統(tǒng)發(fā)生分析 |
| plymouth-theme | 7.0 | Boot splash for Bio-Linux 7 | 開(kāi)機(jī)畫(huà)面程序 |
| prank | 1:1bl1-2 | Multiple alignment software. | 多序列比對(duì)軟件 |
| prevent-upgrade | 0.2 | Stop Bio-Linux from upgrading on release of 12.04 LTS | 防自動(dòng)升級(jí)程序(Ubuntu各版本兼容性差異很大，升級(jí)會(huì)導(dǎo)致很多軟件出錯(cuò)) |
| priam | 2005.07-5 | Generate enzyme-specific profiles for metabolic pathyway prediction | 產(chǎn)生酶特異性譜用于代謝通路預(yù)測(cè) |
| primer3 | 1:1bl-1 | Primer3 picks primers for PCR reactions. | PCR引物設(shè)計(jì) |
| python-cogent | 1:1.4.1bl-1 | Python-cogent, or PyCogent, is a python library for genomic biology. | python基因組生物學(xué)包 |
| qiime | 2:1bl-8 | Quantitative insights into microbial ecology | 定量微生物生態(tài) |
| qtlcart | 1.17f-2 | Map quantitative traits using a map of molecular markers. | 基于分子標(biāo)記的數(shù)量性狀定位 |
| rasmol | 1:1bl-1 | Molecular genetics visualisation tool. | 分子遺傳可視化工具 |
| rbs-finder | 1.0-4 | A program to find Ribosomal binding sites. | rRNA結(jié)合位點(diǎn)預(yù)測(cè) |
| rdp-classifier | 2:1bl1-1 | A niave Bayesian classifier for 16S rRNA sequences. | 基于貝葉斯算法 的16S rRNA分類(lèi) |
| readseq | 1:1bl-3 | Read and reformat biosequences | 生物序列格式轉(zhuǎn)換 |
| sampledata | 20041011-10 | Sample data for Bio-Linux packages | 平臺(tái)測(cè)序數(shù)據(jù)集 |
| samtools | 1:1bl-3 | processing sequence alignments in SAM and BAM formats | SAM/BAM文件轉(zhuǎn)換分析 |
| seaview | 1:1bl1-1 | Multiple sequence alignment editor | 多序列比對(duì)編輯 |
| sequin | 1:1bl-0 | Transitional package that provides bio-linux-ncbi-tools-x11 | 序列提交NCBI客戶(hù)端 |
| shared | 1.1-2 | Some shared files used by Bio-Linux | 共享庫(kù) |
| splitstree | 4.12.6-2 | Analysis and visualisation tool for distance data from biological sequences | 遠(yuǎn)源序列分析 |
| squint | 1.02-4 | Java-based multiple alignment program and editor | 多序列比對(duì)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的用戶(hù)界面 |
| t-coffee | 1:1bl-3 | Multiple Sequence Alignment | 多序列比對(duì) |
| tablet | 1.12.03.26-1 | Graphical viewer for next gen sequence assemblies and alignments | 高通量測(cè)序比對(duì)結(jié)果可視化程序，同Gbrowser |
| taxinspector | 1.0b3-12 | Browser for entries in the NCBI taxonomy database | 生物分類(lèi)數(shù)據(jù) |
| tetra | 1.0b3-1 | tetranucleotide frequency calculator with GUI | 圖型界面的核酸頻率統(tǒng)計(jì) |
| themes | 6.1 | Graphics, icons, wallpaper and a GDM theme for Bio-Linux 6. | 主題v6 |
| themes-v5 | 1.2 | Graphics, icons, KDE splash screen and a GDM theme for Bio-Linux 5. | 主題v5 |
| themes-v7 | 7.0-12 | Graphics, icons, wallpaper and desktop settings for Bio-Linux 7 | 主題v7 |
| transterm-hp | 1:1bl1-1 | finds rho-independent transcription terminators in bacterial genomes | 在細(xì)胞基因組中，查找rho因子不依賴(lài)的轉(zhuǎn)錄終止子 |
| tree-puzzle | 1:1bl-1 | pylogenetic tree reconstruction from molecular sequence | 基于分子序列的系統(tǒng)發(fā)生樹(shù)構(gòu)建 |
| treeview | 1:1bl-1 | A simple program for displaying phylogenies. | 系統(tǒng)發(fā)生/進(jìn)化樹(shù)顯示 |
| trnascan | 1:1bl1-1 | searches for tRNA genes in genomic sequences. | 基因組tRNA預(yù)測(cè) |
| tutorials | 1-23 | Tutorials and documentation for Bio-Linux users. | 幫助文檔 |
| unity-lens | 0.2 | unity lens for Bio-Linux | 搜索濾鏡 |
| usb-maker | 7.0-1 | Script to generate Bio-Linux live memory sticks. | USB版系統(tǒng)定制程序 |
| wise2 | 1:1bl1-2 | Tool for comparison of biopolymers, DNA, and protein sequence. | 比較生物序列聚合物 |
| xcut | 1.4-3 | A re-write of the GNU cut command with many new features. | cut改進(jìn)版 |
| zsh | 1-18 | Z-Shell wrapper package for Bio-Linux. | Z-shell |
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