biolinux是為生物信息學定製的Linux操作系統。
基本介紹
- 中文名：biolinux
- 特點：功能齊全、強大、可定製
- 定製方向：生物信息學
- 門戶頁面：維基百科
簡介,功能,
簡介
Bio-linux由NERC Environmental Bioinformatics Centre開發並維護，詳細內容請訪問bio-linux主頁。
如果你想了解或引用biolinux，請查看或引用關於biolinux的發表在Nature Biotechnology（自然生物技術）上的文章Open Software for biologists: from famine to feast。
功能
Bio-Linux是功能齊全的、強大的、可定製的、易於維護的生物分析工作站。Bio-Linux基於Ubuntu提供500多個生物分析程式，由一個圖形化的選單進行管理，能方便地訪問到其生物分析文檔系統及對測試程式有用的樣本數據。用於處理新型序列數據類型的Bio-Linux軟體包可額外安裝。
最新發生版為Bio-Linux7.0, 基於Ubuntu 12.04 x64版本，發布於2012年11月，安裝程式大小為2G，安裝需要至少15G硬碟空間。
表1. Bio-linux7集成主要生物信息學軟體簡介
| Package | Version | Description | 中文簡介 |
|---|---|---|---|
act | 13.2-1 | A DNA sequence comparison viewer based on Artemis | 基於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測序PCR擴增噪音序列 |
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 | 進化樹查看編輯器 |
artemis | 13.2-6 | Free genome viewer and annotation tool | 免費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. | 生物信息平台重要配置檔案 |
big-blast | 1.0.3-4 | The big-blast script for annotation of long sequences | 注釋長序列的big-blast腳本 |
biocode | 2.3.3-2 | Biocode plugin for Geneious workbench | Geneious workbech的Biocode外掛程式 |
biojava | 1.7.1-3 | Open-source Java framework for processing biological data. | Java生物信息相關包 |
blast | 1:1bl-7 | Rapid searching of nucleotide and protein databases. | 最著名的序列比對軟體 |
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. | 平台軟體說明文檔 |
blixem | 3.1.1-3 | Interactive browser for viewing pairwise Blast results. | 可查看blast結果的互動式瀏覽器 |
cap3 | 20080520-1 | A base calling system | base calling系統，是將測序的圖片結果轉換成序列的過程 *我以前用過cap3的軟體是做序列拼接的，不知這是標錯了，還是另一個軟體 |
catchall | 3.0.1-1 | Analyze data about microbial species abundance | 分析微生物特種豐度數據 |
cd-hit | 2009-1020-1 | a suite of programs designed to quickly group sequences | 序列聚類分組工具箱 |
cdbfasta | 1:20100722bl-3 | FASTA file indexing and retrieval tools | fasta格式序列檔案索引和檢索工具 |
chimeraslayer | 1:20100429bl-4 | chimeric detection utility for 16S rRNA | 16S rRNA混合結果檢測分析工具 |
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 | 雲服務 |
clustal | 1:1bl-7 | Installs clustalw and clustalx for multiple sequence and profile alignments. | |
cytoscape | 1:2.7.0-8 | Platform for visualizing complex-networks and integrating these with attribute data | 著名基因網路分析平台，複雜調控網路、GO分析 |
dendroscope | 1.4.0-5 | Interactive viewer for large phylogenetic trees. | 進化樹查看器 |
denoiser | 1:0.851-9 | Rapid denoising of pyrosequencing amplicon data: exploiting the rank-abundance distribution | 高通量測序擴增噪音去除 |
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 |
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 | 重複序列識別 |
embassy-domainatrix | 0.1.0+20100115-1 | Extra EMBOSS commands to handle domain classification file | EMBOSS工具集：結構域分類 |
embassy-domalign | 0.1.0+20100115-1 | Extra EMBOSS commands for protein domain alignment | EMBOSS工具集：結構域比對 |
embassy-domsearch | 0.1.0++20100115-1 | Extra EMBOSS commands to search for protein domains | EMBOSS工具集：結構域檢索 |
embassy-phylip | 3.69-1 | EMBOSS conversions of the programs in the phylip package | EMBOSS工具集：進化分析 |
emboss | 1:1bl1-1 | extensive set of tools for bioinformatics and biological database management | EMBOSS工具集：資料庫管理 |
emboss-data | 6.3.1-3 | data files for the EMBOSS package | EMBOSS工具集：數據檔案 |
emboss-doc | 6.3.1-3 | documentation for EMBOSS | EMBOSS工具集：說明文檔 |
emboss-lib | 6.3.1-3 | EMBOSS Libraries | EMBOSS工具集：庫檔案 |
emboss-test | 6.3.1-3 | test files for the EMBOSS package | EMBOSS工具集：測試檔案 |
estscan | 2.1-12 | detects coding regions of DNA sequences. | 檢測DNA編碼區 |
exchanger | 1.0-5 | lets you store, annotate and share files via an omixed server | 數據注釋共享服務 |
fasta | 36t2d5-1 | Collection of programs for searching DNA and protein databases. | 類似於blast的序列比對 |
fastdnaml | 1:1bl-2 | estimates maximum likelihood phylogenetic trees from nucleotide sequences | 進化樹分析 |
fastqc | 0.10.1-2 | A quality control application for high throughput sequence data | 高通量測序質量控制軟體 |
fasttree | 2.1.3-1 | Infers approximately-maximum-likelihood phylogenetic trees | 進化樹分析 |
forester | 1.92-10 | ATV (A Tree Viewer) is a Java tool for the visualization of annotated phylogenetic trees. | 進化樹可視化 |
gap2caf | 0.20100408-2 | Handles conversion of gap format assemblies to caf format. | 格式轉換gap為caf |
geneious | 5.5.7-3 | Geneious Basic workbench from Biomatters | 綜合分析平台 |
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，資料庫檢索 |
glimmer3 | 3.02-1 | System for finding genes in microbial DNA. | 微生物基因鑑定 |
handlebar | 2.2.2-7 | Handlebar is a database for storing data about barcodes and acessing the data via a web front-end. | 數據管理資料庫 |
happy | 1.2-2 | Multipoint QTL Mapping in Genetically Heterogeneous Animals | 多點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 |
isacreator | 1.6.0-1 | GUI to import and edit ISA dataset descriptions. | ISA數據描述導入與編輯 |
jalview | 1:2.7.0-2 | a Java multiple alignment editor | Java多比對編輯器 |
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 |
jprofilegrid | 1:1bl-2 | Multiple sequence alignment tool that generates ProfileGrids | |
keyring | 5 | Public key package for the Bio-Linux package repository | Bio-linux軟體包 |
libajax6 | 6.3.1-3 | EMBOSS library for commands | EMBOSS庫 |
libajax6-dev | 6.3.1-3 | development files for libajax | libajax開發檔案 |
libnucleus6 | 6.3.1-3 | EMBOSS library for molecular sequence analysis | EMBOSS庫：分子序列分析 |
libnucleus6-dev | 6.3.1-3 | development files for libnucleus | libnucleus開發檔案 |
lucy | 1:1bl-1 | Preparation of raw DNA sequence fragments for sequence assembly. | 原始DNA序列處理用於組裝 |
mcl | 1:1bl-2 | Tools for clustering protein groups in to protein families. | 蛋白家族聚類 |
mesquite | 2.74-3 | Software for evolutionary biology. | |
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相關包 |
mrbayes | 1:2bl-3 | Bayesian estimation of phylogeny | |
mrbayes-multi | 3.1.2-4 | Multiprocessor version of MrBayes | 多執行緒版的MrBayes |
msatfinder | 2.0.10-1 | Microsatellite Finder | 鑑定微衛星 |
mspcrunch | 2.5-1 | a BLAST post-processing filter. | blast結果分析 |
mummer | 1:1bl-1 | a system for rapidly aligning entire genomes. | 序列比對 |
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. | 序列檢索結果的多序列比對瀏覽器 |
ncbi-tools-x11 | 1:1bl-3 | NCBI libraries for biology applications (X-based utilities) | NCBI庫 |
njplot | 1:1bl-2 | Phylogenetic tree drawing program. | 系統發育樹 |
nrdb | 2-1 | Generates quasi-nonredundant protein and nucleotide sequence databases. | 產生類似非冗餘蛋白和核酸序列資料庫 |
ocount | 0.5-1 | Oligonucleotide frequency counter | 寡核苷酸頻率統計 |
oligoarray | 2.1-11 | Computes oligonucleotides for microarray construction | 晶片設計 |
oligoarrayaux | 3.7-1 | Free software that is required for the OligoArray2.1 software. | 晶片設計升級版 |
omegamap | 0.5-1 | Detects natural selection and recombination in DNA or RNA sequences. | 檢測DNA/RNA序列自然選擇和重組 |
paml | 1:1bl1 | Phylogenetic analysis for DNA/protein sequences using max. likelihood | 最大似然數法的蛋白/核酸系統發生分析 |
pfaat | 1.0.034-7 | Sequence alignment editor designed for protein family analysis. | 蛋白家族的多序列比對分析 |
phylip | 1:1bl-2 | Tool for inferring phylogenies. | 系統發生分析 |
phyml | 1:1bl-1 | Phylogeny software based on the maximum-likelihood principle. | 最大似然數法的系統發生分析 |
plymouth-theme | 7.0 | Boot splash for Bio-Linux 7 | 開機畫面程式 |
prank | 1:1bl1-2 | Multiple alignment software. | 多序列比對軟體 |
prevent-upgrade | 0.2 | Stop Bio-Linux from upgrading on release of 12.04 LTS | |
priam | 2005.07-5 | Generate enzyme-specific profiles for metabolic pathyway prediction | 產生酶特異性譜用於代謝通路預測 |
primer3 | 1:1bl-1 | Primer3 picks primers for PCR reactions. | PCR引物設計 |
python-cogent | 1:1.4.1bl-1 | Python-cogent, or PyCogent, is a python library for genomic biology. | python基因組生物學包 |
qiime | 2:1bl-8 | Quantitative insights into microbial ecology | 定量微生物生態 |
qtlcart | 1.17f-2 | Map quantitative traits using a map of molecular markers. | |
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結合位點預測 |
rdp-classifier | 2:1bl1-1 | A niave Bayesian classifier for 16S rRNA sequences. | 基於貝葉斯算法 的16S rRNA分類 |
readseq | 1:1bl-3 | Read and reformat biosequences | 生物序列格式轉換 |
sampledata | 20041011-10 | Sample data for Bio-Linux packages | 平台測序數據集 |
samtools | 1:1bl-3 | processing sequence alignments in SAM and BAM formats | SAM/BAM檔案轉換分析 |
seaview | 1:1bl1-1 | Multiple sequence alignment editor | 多序列比對編輯 |
sequin | 1:1bl-0 | Transitional package that provides bio-linux-ncbi-tools-x11 | 序列提交NCBI客戶端 |
shared | 1.1-2 | Some shared files used by Bio-Linux | 共享庫 |
splitstree | 4.12.6-2 | Analysis and visualisation tool for distance data from biological sequences | 遠源序列分析 |
squint | 1.02-4 | Java-based multiple alignment program and editor | 多序列比對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的用戶界面 |
t-coffee | 1:1bl-3 | Multiple Sequence Alignment | 多序列比對 |
tablet | 1.12.03.26-1 | Graphical viewer for next gen sequence assemblies and alignments | 高通量測序比對結果可視化程式，同Gbrowser |
taxinspector | 1.0b3-12 | Browser for entries in the NCBI taxonomy database | 生物分類數據 |
tetra | 1.0b3-1 | tetranucleotide frequency calculator with GUI | 圖型界面的核酸頻率統計 |
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 | |
tree-puzzle | 1:1bl-1 | pylogenetic tree reconstruction from molecular sequence | 基於分子序列的系統發生樹構建 |
treeview | 1:1bl-1 | A simple program for displaying phylogenies. | 系統發生/進化樹顯示 |
trnascan | 1:1bl1-1 | searches for tRNA genes in genomic sequences. | 基因組tRNA預測 |
tutorials | 1-23 | Tutorials and documentation for Bio-Linux users. | 幫助文檔 |
unity-lens | 0.2 | unity lens for Bio-Linux | 搜尋濾鏡 |
usb-maker | 7.0-1 | Script to generate Bio-Linux live memory sticks. | USB版系統定製程式 |
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改進版 |
zsh | 1-18 | Z-Shell wrapper package for Bio-Linux. | Z-shell |
