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
act13.2-1A DNA sequence comparison viewer based on Artemis基于Artemis的DN序列可视化比较工具
ampliconnoise1bl-0Programs for the removal of noise from 454 sequenced PCR amplicons去除454测序PCR扩增噪音序列
arb1:1bl1-3Graphical sequence and data analysis tools.图形化序列分析工具
archaeopteryx0.972.beta9M-3A phylogenetic tree viewer and editor进化树查看编辑器
artemis13.2-6Free genome viewer and annotation tool免费的本地基因组浏览器
assembly-conversion-tools0.01-10Conversion tools for handling 454 assemblies.454序列拼接转换工具
backups0.3-6Bio-Linux 5/6 backup utilities.biolinx5/6旧版本支持组件
base-directories1.0-37Essential Bio-Linux configuration files.生物信息平台重要配置文件
big-blast1.0.3-4The big-blast script for annotation of long sequences注释长序列的big-blast脚本
biocode2.3.3-2Biocode plugin for Geneious workbenchGeneious workbech的Biocode插件
biojava1.7.1-3Open-source Java framework for processing biological data.Java生物信息相关包
blast1:1bl-7Rapid searching of nucleotide and protein databases.最著名的序列比对软件
blast+1:1bl1Blast+ contains new builds of the popular blast family of programs from the NCBI.blast的衍生版
bldp-files1.1-96Documentation for bioinformatics software on Bio-Linux.平台软件说明文档
blixem3.1.1-3Interactive browser for viewing pairwise Blast results.可查看blast结果的交互式浏览器
cap320080520-1A 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
catchall3.0.1-1Analyze data about microbial species abundance分析微生物特种丰度数据
cd-hit2009-1020-1a suite of programs designed to quickly group sequences序列聚类分组工具箱
cdbfasta1:20100722bl-3FASTA file indexing and retrieval toolsfasta格式序列文件索引和检索工具
chimeraslayer1:20100429bl-4chimeric detection utility for 16S rRNA16S rRNA混合结果检测分析工具
clcsequenceviewer6.4-1CLC Free Sequence ViewerCLC序列查看器
cloudbl-desktop1.4Adds useful links to the remote desktop for Cloud BL云服务
clustal1:1bl-7Installs clustalw and clustalx for multiple sequence and profile alignments.多序列比对
cytoscape1:2.7.0-8Platform 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
dendroscope1.4.0-5Interactive viewer for large phylogenetic trees.进化树查看器
denoiser1:0.851-9Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distribution高通量测序扩增噪音去除
dialign1:1bl-2Segment-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
dotter3.1-1Graphical dotplot program for detailed comparison of two sequences两序列dotplot图比较
dust2bl1-2Repetitive sequence masker重复序列识别
embassy-domainatrix0.1.0+20100115-1Extra EMBOSS commands to handle domain classification fileEMBOSS工具集:结构域分类
embassy-domalign0.1.0+20100115-1Extra EMBOSS commands for protein domain alignmentEMBOSS工具集:结构域比对
embassy-domsearch0.1.0++20100115-1Extra EMBOSS commands to search for protein domainsEMBOSS工具集:结构域检索
embassy-phylip3.69-1EMBOSS conversions of the programs in the phylip packageEMBOSS工具集:进化分析
emboss1:1bl1-1extensive set of tools for bioinformatics and biological database managementEMBOSS工具集:数据库管理
emboss-data6.3.1-3data files for the EMBOSS packageEMBOSS工具集:数据文件
emboss-doc6.3.1-3documentation for EMBOSSEMBOSS工具集:说明文档
emboss-lib6.3.1-3EMBOSS LibrariesEMBOSS工具集:库文件
emboss-test6.3.1-3test files for the EMBOSS packageEMBOSS工具集:测试文件
estscan2.1-12detects coding regions of DNA sequences.检测DNA编码区
exchanger1.0-5lets you store, annotate and share files via an omixed server数据注释共享服务
fasta36t2d5-1Collection of programs for searching DNA and protein databases.类似于blast的序列比对
fastdnaml1:1bl-2estimates maximum likelihood phylogenetic trees from nucleotide sequences进化树分析
fastqc0.10.1-2A quality control application for high throughput sequence data高通量测序质量控制软件
fasttree2.1.3-1Infers approximately-maximum-likelihood phylogenetic trees进化树分析
forester1.92-10ATV (A Tree Viewer) is a Java tool for the visualization of annotated phylogenetic trees.进化树可视化
gap2caf0.20100408-2Handles conversion of gap format assemblies to caf format.格式转换gap为caf
geneious5.5.7-3Geneious Basic workbench from Biomatters综合分析平台
geneious-genbanksubmit1.3.0-1GenBank submission for Geneious workbench序列提交工具
genquery2.2.4-3GenQuery is a set of Perl libraries for managing SQL query templates and making web-based query forms.Perl包,数据库检索
glimmer33.02-1System for finding genes in microbial DNA.微生物基因鉴定
handlebar2.2.2-7Handlebar is a database for storing data about barcodes and acessing the data via a web front-end.数据管理数据库
happy1.2-2Multipoint QTL Mapping in Genetically Heterogeneous Animals多点QTL作图
hmmer1:1bl-1HMM methods for searching databases for multiple sequence alignments隐马方式的多序列比对
isacreator1.6.0-1GUI to import and edit ISA dataset descriptions.ISA数据描述导入与编辑
jalview1:2.7.0-2a Java multiple alignment editorJava多比对编辑器
jemboss6.3bl1-8graphical user interface to EMBOSSEMBOSS图形界面
jmotu1.0.6-2Clusters barcode DNA sequence data into molecular operational taxonomic unitsDNA序列聚类
jprofilegrid1:1bl-2Multiple sequence alignment tool that generates ProfileGrids多序列比对
keyring5Public key package for the Bio-Linux package repositoryBio-linux软件包
libajax66.3.1-3EMBOSS library for commandsEMBOSS库
libajax6-dev6.3.1-3development files for libajaxlibajax开发文件
libnucleus66.3.1-3EMBOSS library for molecular sequence analysisEMBOSS库:分子序列分析
libnucleus6-dev6.3.1-3development files for libnucleuslibnucleus开发文件
lucy1:1bl-1Preparation of raw DNA sequence fragments for sequence assembly.原始DNA序列处理用于组装
mcl1:1bl-2Tools for clustering protein groups in to protein families.蛋白家族聚类
mesquite2.74-3Software for evolutionary biology.进化生物学
mira1:1bl-2Assembly 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-party1:1bl-1Provides useful script for sequence handling序列处理
mothur2bl-5This is a wrapper package for mothurmothus相关包
mrbayes1:2bl-3Bayesian estimation of phylogeny基于贝叶斯估计的系统发育分析
mrbayes-multi3.1.2-4Multiprocessor version of MrBayes多线程版的MrBayes
msatfinder2.0.10-1Microsatellite Finder鉴定微卫星
mspcrunch2.5-1a BLAST post-processing filter.blast结果分析
mummer1:1bl-1a system for rapidly aligning entire genomes.序列比对
muscle1:1bl-2Bio-Linux wrapper for the Debian Med muscle packagemed muscle包
mview1.51-3Multiple alignment viewer for sequence database search results.序列检索结果的多序列比对浏览器
ncbi-tools-x111:1bl-3NCBI libraries for biology applications (X-based utilities)NCBI库
njplot1:1bl-2Phylogenetic tree drawing program.系统发育树
nrdb2-1Generates quasi-nonredundant protein and nucleotide sequence databases.产生类似非冗余蛋白和核酸序列数据库
ocount0.5-1Oligonucleotide frequency counter寡核苷酸频率统计
oligoarray2.1-11Computes oligonucleotides for microarray construction芯片设计
oligoarrayaux3.7-1Free software that is required for the OligoArray2.1 software.芯片设计升级版
omegamap0.5-1Detects natural selection and recombination in DNA or RNA sequences.检测DNA/RNA序列自然选择和重组
paml1:1bl1Phylogenetic 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
pfaat1.0.034-7Sequence alignment editor designed for protein family analysis.蛋白家族的多序列比对分析
phylip1:1bl-2Tool for inferring phylogenies.系统发生分析
phyml1:1bl-1Phylogeny software based on the maximum-likelihood principle.最大似然数法的系统发生分析
plymouth-theme7.0Boot splash for Bio-Linux 7开机画面程序
prank1:1bl1-2Multiple alignment software.多序列比对软件
prevent-upgrade0.2Stop 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)
priam2005.07-5Generate enzyme-specific profiles for metabolic pathyway prediction产生酶特异性谱用于代谢通路预测
primer31:1bl-1Primer3 picks primers for PCR reactions.PCR引物设计
python-cogent1:1.4.1bl-1Python-cogent, or PyCogent, is a python library for genomic biology.python基因组生物学包
qiime2:1bl-8Quantitative insights into microbial ecology定量微生物生态
qtlcart1.17f-2Map quantitative traits using a map of molecular markers.基于分子标记的数量性状定位
rasmol1:1bl-1Molecular genetics visualisation tool.分子遗传可视化工具
rbs-finder1.0-4A program to find Ribosomal binding sites.rRNA结合位点预测
rdp-classifier2:1bl1-1A niave Bayesian classifier for 16S rRNA sequences.基于贝叶斯算法 的16S rRNA分类
readseq1:1bl-3Read and reformat biosequences生物序列格式转换
sampledata20041011-10Sample data for Bio-Linux packages平台测序数据集
samtools1:1bl-3processing sequence alignments in SAM and BAM formatsSAM/BAM文件转换分析
seaview1:1bl1-1Multiple sequence alignment editor多序列比对编辑
sequin1:1bl-0Transitional package that provides bio-linux-ncbi-tools-x11序列提交NCBI客户端
shared1.1-2Some shared files used by Bio-Linux共享库
splitstree4.12.6-2Analysis and visualisation tool for distance data from biological sequences远源序列分析
squint1.02-4Java-based multiple alignment program and editor多序列比对java版
staden2006.1.7.0+1.11.6-8A suite of tools for sequence analysis.序列分析工具集
stars1.2a-12STARS is an alternative interface to Staden.staden的用户界面
t-coffee1:1bl-3Multiple Sequence Alignment多序列比对
tablet1.12.03.26-1Graphical viewer for next gen sequence assemblies and alignments高通量测序比对结果可视化程序,同Gbrowser
taxinspector1.0b3-12Browser for entries in the NCBI taxonomy database生物分类数据
tetra1.0b3-1tetranucleotide frequency calculator with GUI图型界面的核酸频率统计
themes6.1Graphics, icons, wallpaper and a GDM theme for Bio-Linux 6.主题v6
themes-v51.2Graphics, icons, KDE splash screen and a GDM theme for Bio-Linux 5.主题v5
themes-v77.0-12Graphics, icons, wallpaper and desktop settings for Bio-Linux 7主题v7
transterm-hp1:1bl1-1finds 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-puzzle1:1bl-1pylogenetic tree reconstruction from molecular sequence基于分子序列的系统发生树构建
treeview1:1bl-1A simple program for displaying phylogenies.系统发生/进化树显示
trnascan1:1bl1-1searches for tRNA genes in genomic sequences.基因组tRNA预测
tutorials1-23Tutorials and documentation for Bio-Linux users.帮助文档
unity-lens0.2unity lens for Bio-Linux搜索滤镜
usb-maker7.0-1Script to generate Bio-Linux live memory sticks.USB版系统定制程序
wise21:1bl1-2Tool for comparison of biopolymers, DNA, and protein sequence.比较生物序列聚合物
xcut1.4-3A re-write of the GNU cut command with many new features.cut改进版
zsh1-18Z-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
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  • 分类:linux

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