服务器评测
常言道：“工欲善其事，必先利其器”。国内多数计算机用户使用的都是Windows操作系统，甚至连科研单位也在所难免。出现这样的情况原因很多，对于一个Bio-technician而言，离不开Win的一个很大的原因是所用的专业软件运行平台离不开它。实际上，很多科研软件都是先有*nix版本的，或者有些就只有那些版本。本人之前也一直很痛苦在Ubuntu上用不了DANMAN（在Ubuntu 8.04的时侯我Wine过，但Ubuntu 9.04时侯就完全用不了了）。其实，Ubuntu的源里面就有很多这样的软件。
命令：
yuanjin@yuanjin-laptop:~$ apt-cache DNA >DNA.txt
//根据软件的描述来搜索关键词“DNA”，返回的结果输出到文本DNA.txt
yuanjin@yuanjin-laptop:~$ gedit DNA.txt
//用gedit打开文本DNA.txt后就可以根据自己需要寻找软件了。
PS：返回的结果中有部份可能会与DNA毫无关系，但是搜索到的东西比新德立软件管理器中搜到的多多了。
附－筛选过之后的搜索结果（搞我们这行的，估计这些外文都不是问题了，有兴趣自己看。重点推荐Ugene这款功能相对强悍的整合软件工具包，访问主页）。
boxshade – Pretty-printing of multiple sequence alignments
dialign – Segment-based multiple sequence alignment
dialign-tx – Segment-based multiple sequence alignment
exonerate – generic tool for pairwise sequence comparison
fastdnaml – Tool for construction of phylogenetic trees of DNA sequences
last-align – genome-scale comparison of biological sequences
maq – maps short fixed-length polymorphic DNA sequence reads to reference sequences
melting – computing the melting temperature of nucleic acid duplex
mummer – Efficient sequence alignment of full genomes
ncbi-epcr – Tool to test a DNA sequence for the presence of sequence tagged sites
plink – whole-genome association analysis toolset
primer3 – Tool to design flanking oligo nucleotides for DNA amplification
sibsim4 – align expressed RNA sequences on a DNA template
sigma-align – Simple greedy multiple alignment of non-coding DNA sequences
sim4 – tool for aligning cDNA and genomic DNA
t-coffee – Multiple Sequence Alignment
tigr-glimmer – Gene detection in archea and bacteria
ugene – integrated bioinformatics toolkit
ugene-data – required data for UGENE – integrated bioinformatics toolkit
wise – comparison of biopolymers, commonly DNA and protein sequences
wise-doc – documentation for the wise package
clustalw – global multiple nucleotide or peptide sequence alignment
molphy – Program Package for MOLecular PHYlogenetics
BioInfoServOS Ubuntu下的生物信息整合系统
主页：http://www.bioinfoserv.org/BioLinux/
概括：基于ubuntu的linux系统，主要包含GUI、CommandLine和web应用的生物软件。
开发团队：
Mingwei LiuMingwei Liu: 现供职于重庆医科大学，是BioInfoServOS计划的发起和执行者。他的努力是BioInfoServOS得以出现的主因。
更多：http://www.bioinfoserv.org/BioLinux/modules/wordpress/?page_id=2
BioInfoServOS是一个基于x86平台的生物信息快速部署平台系统，旨在解决目前生命科学研究在生物信息分析及其开发环境快速部署上的需求瓶颈，为生物信息分析及其开发环境的快速部署提供整套解决方案，让生命科学研究者无需专业培训和技术学习就能快速获得稳定、高效、界面友好的生物信息管理与数据分析终端操作界面以及强大的生物软件开发环境。
同时，BioInfoServOS亦能完美顺畅实现日常办公、网络冲浪、影音娱乐以及文档演示等日常需求，能带来Microsoft Windows系统所从没有过的个性化愉悦体验和高效率冲击。由于具有linux固有的特性，BioInfoServOS还可以让您远离病毒频繁攻击和漏洞缺陷侵扰等烦恼，极大地提高您日常工作以及生命科学研究的效率和成效，极大地减少您在系统管理和软件选择上的支出与开销。
BioInfoServOS基于xUbuntu，能完美支持桌面电脑、笔记本电脑和服务器硬件，其界面友好，功能强大，易于快速安装部署。
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.
更详细的介绍：
http://www.bioinfoserv.org/BioLinux/uploads/bioinfoservFAQ/bioinfoserv/softIntroduction.html
