bio-linux
http://www.bioinfoserv.org/BioLinux/
http://bioinformatics.rri.sari.ac.uk/bioinformatics/
http://bioknoppix.hpcf.upr.edu/screenshots/photoalbum_view
http://envgen.nox.ac.uk/bio-linux/
http://envgen.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
Bio-Linux – Bioinformatics Tools for Linux
Published
by
on March 7, 2008
in linux and noteworthy
. Tags: bioinformatics, howto, linux, ubuntu.
Bio-Linux is a specialised Linux disro that provides both standard and cutting edge bioinformatics software tools on a Linux base.
I wrote a post on my old blog a little while back now detailing how to use the packages from Bio-Linux in Ubuntu Linux, but it got missed in the migration (sorry to all those who have been searching for it). Here’s a repost and update for Ubuntu 7.10…
Log into your system and open up a terminal, then follow these steps…
sudo gedit /etc/apt/sources.list
Add the following lines to the end of the file:
# Bio-Linux package repository
deb http://envgen.nox.ac.uk/bio-linux/ unstable bio-linux
Save and close the file, now back at the terminal type the following:1
sudo apt-get update
sudo apt-get install bio-linux-base-directories bio-linux-staden
Next step is to set-up your environment for Bio-Linux…
sudo gedit /etc/bash.bashrc
Add the following lines to the end of the file:
# Set up Bio-Linux Environment
source /usr/local/bioinf/config_files/aliasrc
source /usr/local/bioinf/config_files/bioenvrc
Save and close the file.
That’s it, now all of the packages available through Bio-Linux are now available to you in Ubuntu. One final word of warning… I’ve noticed that a few of the packages are a little out of date, (the Bio-Linux version of Taverna is 1.4, but 1.7 is now available)2 so it might be worth checking the version numbers before installing things.
- Note that we need to install the
bio-linux-stadenpackage, without this we’d have to do a bit more hacking in config files to stop getting errors whenever we open up a terminal. ↩ - The other thing to note with the Bio-Linux version of Taverna – it doesn’t start properly without a little bit of hacking…
(If you decided to go with the Bio-Linux version, you can launch it by running the following in the terminal: /usr/local/bioinf/taverna/taverna/runme.sh). ↩
主要包含GUI、CommandLine和web应用的生物软件：
GUI的软件， 主要是图形界面操作的生物软件，目前主要安装利用bioinfoserv软件仓库进行安装，如Jemboss, Staden等。
CommandLine软件， 它不需要图形操作界面的，事实上在Jemboss中基本都包含了，不过这种方式可以更好地进行参数选择，从而更有利于控制程序的运行效率，如blast， clustw, QTLChart等，系统没有默认安装，不过安装十分容易，参看下面的“生 物软件的搜索与安装”。
Web应用的软件， 主要是利用网络服务器apache/apache2和jsp, php, perl等脚本语言来支持运行的程序，使用的时候之需要打开浏览器，就可以轻松地使用软件，这种软件部署方式主要是为了利于程序的共享使用。其效率受网络 速度和程序编写的可靠性影响。本系统在/var/www/biotools下具有多个web应用软件，如InterproScan(jips)，wEMBOSS,phpPhyloTree, Sequence Manipulation Suite，这些均可直接从菜单打开，而且您还可以扩展web应用的生物软件， 方法是将web应用软件拷贝到这个目录，然后安装它们各自的安装和使用浏览器方式启动。
当然还有些生物软件应用充分地结合了浏览器，特别是firefox的插件。现在有较多的生物软件应用被写成了插件直接安装到firefox中，极大地方便 了使用者，如biobar, biofox和 zotero等。本系统浏览器已经安装好这些插件。
以下是相关生物软件的说明,没有具体翻译过来了,因为 有些语句实在翻译得不贴切,再说既然您是生物专业的使用者,这些英文理解起来也是小儿科了：
bioinfoserv-act – ACT (Artemis Comparison Tool) is a DNA sequence comparison viewer based on Artemis
bioinfoserv-ape – APE (Analyses of Phylogenetics and Evolution) is a package written in R. APE aims to be both a computing tool to analyse phylogenetic and evolutionary data, and an environment to develop and implement new analytical methods.
bioinfoserv-arb – The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis.
bioinfoserv-artemis – Artemis is a free genome viewer and annotation tool
bioinfoserv-base-directories – Initial bioinfoserv package which creates directories, installs configuration and support files for bioinfoserv.
bioinfoserv-big-blast – This script will chop up a large sequence, run blast on each bit and then write out an EMBL feature table and a MSPcrunch -d file containing the hits.
bioinfoserv-biojava – BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It include objects for manipulating sequences, file parsers, DAS client and server suport, access to BioSQL and Ensembl databases, and powerful analysis and statistical routines including a dynamic programming toolkit.
bioinfoserv-blast – BLAST 2.2.15, (Basic Local Alignment Search Tool), provides a method for rapid searching of nucleotide and protein databases.
bioinfoserv-bldp-files – bioinfoserv package providing organised searching facilities and access to bioinformatics software descriptions and documentation, including links to homepages, remote and local documentation.
bioinfoserv-blixem – blixem, which stands for BLast matches In an X-windows Embedded Multiple alignment, is an interactive browser of pairwise Blast matches that have been stacked up in a master-slave multiple alignment.
bioinfoserv-cap3 – A base calling system.
bioinfoserv-clcworkbench – CLC Free Workbench is a graphical interface allowing the user to carry out many basic bioinformatics tasks.
bioinfoserv-clustal – Clustal X is a new windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analysing the results.
bioinfoserv-coalesce – Fits the model which has a single population of constant size, and estimates 4Nu, where N is the effective population size and u is the neutral mutation rate per site.
bioinfoserv-documentation – Centralised documentation folder for bioinformatics software on bioinfoserv
bioinfoserv-dotter – Dotter is a graphical dotplot program for detailed comparison of two sequences.
bioinfoserv-dust – Dust – repetitive sequence masker
bioinfoserv-eclipse – Eclipse is a kind of universal tool platform – an open extensible IDE for anything and nothing in particular.
bioinfoserv-emboss – Emboss contains an extensive set of tools for bioinformatics and biological database management.
bioinfoserv-emboss-kmenus – Window manager menus and wrappers scripts for EMBOSS written by Thomas Siegmund (http://userpage.fu-berlin.de/~sgmd/)
bioinfoserv-envbase-for-pedro – This adds the necessary settings and template for Pedro to edit EnvBase files, including integration with TaxInspector and an icon for you to click.
bioinfoserv-estferret – ESTFerret processes, clusters and annotates EST data.
bioinfoserv-estscan – ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. It will also detect and correct sequencing errors that lead to frameshifts.
bioinfoserv-fastDNAml – fastDNAml is a program for estimating maximum likelihood phylogenetic trees from nucleotide sequences.
bioinfoserv-fasta – FASTA contains many programs for searching DNA and protein databases and for evaluating statistical significance from randomly shuffled sequences.
bioinfoserv-fluctuate – Fits the model which has a single population which has been growing (or shrinking) according to an exponential growth law.
bioinfoserv-forester – ATV (A Tree Viewer) is a Java tool for the visualization of annotated phylogenetic trees.
bioinfoserv-genquery – GenQuery is a set of Perl libraries for managing SQL query templates and making web-based query forms.
bioinfoserv-glimmer – Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses.
bioinfoserv-gsrint – Scripts for use within GeneSpring
bioinfoserv-handlebar – Handlebar (previously known as BarcodeBase) is a database for storing data about barcodes and acessing the data via a web front-end.
bioinfoserv-happy – HAPPY: a software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals
bioinfoserv-hmmer – HMMER is an implementation of profile HMM methods for sensitive database searches using multiple sequence alignments as queries.
bioinfoserv-jalview – Jalview is a Java multiple alignment editor
bioinfoserv-lamarc – Estimates population parameters using Likelihood Analysis using Random Coalescence.
bioinfoserv-lucy – Lucy is a utility that prepares raw DNA sequence fragments for sequence assembly, possibly using the TIGR Assembler. The cleanup process includes quality assessment, confidence reassurance, vector trimming and vector removal.
bioinfoserv-maxd – maxd is a data warehouse and visualisation environment for genomic expression data.
bioinfoserv-mcl – TribeMCL is a method for clustering proteins into related groups, which are termed ‘protein families’. This clustering is achieved by analysing similarity patterns between proteins in a given dataset, and using these patterns to assign proteins into related groups. In many cases, proteins in the same protein familywill have similar functional properties. TribeMCL uses a novel clustering method (Markov Clustering or MCL) which solves problems which normally hinder protein sequence clustering. These problems include: multi-domain proteins, peptide fragments and proteins which possess domains which are very widespread (promiscuous domains). The efficiency of the method makes it applicable to the clustering of very large datasets.
bioinfoserv-mesquite – Mesquite is software for evolutionary , designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis.
bioinfoserv-migrate – Estimates effective population sizes and past migration rates between n populations.
bioinfoserv-mountapp – Mountapp provides a small docked area for mounting filesystems
bioinfoserv-mrbayes – MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations.
bioinfoserv-mrbayes-multi – MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. This version has been compiled to run on multiple processors.
bioinfoserv-msatfinder – Microsatellite Finder
bioinfoserv-mspcrunch – MSPcrunch is a BLAST post-processing filter.
bioinfoserv-mummer – MUMmer is a system for rapidly aligning entire genomes.
bioinfoserv-muscle – A bioinfoserv wrapper for the muscle package maintained by Steffan Moeller.
bioinfoserv-mview – MView is a tool for converting the results of a sequence database search (BLAST, FASTA, etc.) into the form of a coloured multiple alignment of hits stacked against the query. Alternatively, an existing multiple alignment (MSF, PIR, CLUSTAL, etc.) can be processed.
bioinfoserv-netblast – NetBLAST searches for sequences similar to a query sequence. The query and the database searched can be either peptide or nucleic acid in any combination. NetBLAST can search only databases maintained at the National Center for Biotechnology Information (NCBI) in Bethesda, Maryland, USA.
bioinfoserv-njplot – NJPLOT is a phylogenetic tree drawing program that handles files describing trees by the nested parentheses method.
bioinfoserv-nrdb – nrdb can be used to generate quasi-nonredundant protein and nucleotide sequence databases.
bioinfoserv-ocount – Ocount – oligonucleotide frequency counter.
bioinfoserv-oligoarray – OligoArray 2.1 is free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction.
bioinfoserv-oligoarrayaux – OligoArrayAux 2.1 is free software that is required for the OligoArray2.1 software.
bioinfoserv-omegamap – OmegaMap is a program for detecting natural selection and recombination in DNA or RNA sequences.
bioinfoserv-paml – PAML is a program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang.
bioinfoserv-partigene – PartiGene is used to cluster sequences and run initial blast searches for basic annotation purposes.
bioinfoserv-pedro – Pedro is an application that creates data entry forms based on a data model written in a particular style of XML Schema.
bioinfoserv-peptidemapper – PeptideMapper is a simple peptide mapping tool written by Rob Beynon, Protein Function Group, University of Liverpool. This presentation tool generates SVG files. The homepage for this package is: http://www.liv.ac.uk/pfg/Tools.html
bioinfoserv-pfaat – The Pfaat protein family alignment annotation tool is a Java-based multiple sequence alignment editor and viewer designed for protein family analysis. The application merges display features such as dendrograms, secondary and tertiary protein structures.
bioinfoserv-pftools – The ‘pftools’ package is a collection of experimental programs supporting the generalized profile format and search method of PROSITE.
bioinfoserv-phylip – PHYLIP is a free package of programs for inferring phylogenies. It is distributed as source code, documentation files, and a number of different types of executables.
bioinfoserv-prank – Prank is multiple alignment software as described in the paper “An algorithm for progressive multiple alignment of sequences with insertions” (PNAS 102:10557–10562). The author of the software is Ari Loytynoja (ari@ebi.ac.uk).
bioinfoserv-priam – Priam – a program to generate enzyme-specific profiles for metabolic pathyway prediction.
bioinfoserv-primer3 – Primer3 picks primers for PCR reactions.
bioinfoserv-prot4est – prot4EST is designed to translate error-prone nucleotide sequences producing robust polypeptide predictions.
bioinfoserv-qtlcart – QTL Cartographer is a suite of programs to map quantitative traits using a map of molecular markers.
bioinfoserv-rasmol – RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images.
bioinfoserv-rbs-finder – A program to find Ribosomal binding sites.
bioinfoserv-readseq – Read & reformat biosequences, Java command-line version.
bioinfoserv-recombine – Fits a model which has a single population of constant size with a single recombination rate across all sites.
bioinfoserv-sampledata – Sample data for bioinfoserv packages
bioinfoserv-seaview – SeaView is a graphical multiple sequence alignment editor developped by Manolo Gouy. SeaView is able to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to manually edit the alignment, and also to run DOT-PLOT or CLUSTALW programs to locally improve the alignment.
bioinfoserv-sequin – Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank, EMBL, or DDBJ sequence databases.
bioinfoserv-splitstree – SplitsTree uses the split decomposition method to analyze and visualize distance data, especially extracted from biological sequences
bioinfoserv-staden – Staden is a suite of tools for bioinformatics analysis.
bioinfoserv-stars – STARS is an alternative interface to staden for studying polymorphisms in short sequences with batch processing, manual editing, trace viewing and data management. STARS was initially designed for Multi Locus Sequence Typing of bacteria.
bioinfoserv-t-coffee – T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can mix sequences and structures.
bioinfoserv-taverna – Taverna is a graphical client for setting up workflows that make use of web services.
bioinfoserv-taxinspector – TaxInspector is a browser for entries in the NCBI taxonomy database.
bioinfoserv-tetra – TETRA – tetranucleotide frequency calculator with GUI.
bioinfoserv-themes – Graphics, icons, KDE splash screen and a GDM theme for bioinfoserv.
bioinfoserv-trace2dbest – Processes trace files into dbEST submissions
bioinfoserv-transterm – Ocount – oligonucleotide frequency counter.
bioinfoserv-transterm-hp – Ocount – oligonucleotide frequency counter.
bioinfoserv-tree-puzzle – TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch.
bioinfoserv-treeview – TreeView is a simple program for displaying phylogenies.
bioinfoserv-trnascan – tRNAscan-SE searches for tRNA genes in genomic sequences.
bioinfoserv-wise2 – Wise2 is a package focused on comparisons of biopolymers, commonly DNA sequence and protein sequence.
bioinfoserv-yamap – Yet Another Microbial Annotation Pipeline.
