一个合适好用的应用软件对于生物科研者来说如同一把利剑，帮您打开科研的大门并为您的科研

之路保驾护航！这里整理收集了一些生物软件，欢迎大家积极跟贴更新，并提出建议。同时希望

大家积极跟贴交流使用过程中的宝贵经验！

这里介绍的软件均为免费软件、共享软件或可以使用演示版的商业软件。没有特别说明，均为

windows应用软件，在win98及以上版本都可以使用。软件均可以在基因酷的ftp上能下载（小

于1M的请直接在附件上下载）:

ftp://www.genecool.com:2121 ，用户名和密码均为：genecool。

由于只有部分版主和管理员有ftp上传的权限，如果您有软件或相关资料欲与大家分享，请与管理

员flashhyh联系，或直接Email：genecoolftp@126.com。



部分软件源于生物软件网，在此感谢！

软件名称：DNAuser 1.0

软件大小：1.6M

简介：一个简单的多功能DNA序列分析软件，由DNAClub更新而来。该软件的开发者为陈雄风研究员。

原始网址：http://www.estarray.org/software/default.asp

软件名称：JaMBW 1.1

软件大小：1.6M

简介：JaMBW是一个分子生物学软件包，功能包括：序列格式转换、求序列的补体序列与逆序列、将DNA序列翻译成蛋白序列、序列分析、 多序列比较、特征位点查找、3维分子结构查看、PCR引物设计、缓冲液设计等功能，包含了分子生物学研究常用的一些操作。它一个用Java语言编写的软件，可以跨操作平台使用，是要系统有支持Java语言的环境即可。在windows环境下，几乎所有的浏览器都支持Java语言。JaMBW是一个非常出色的工具软件！

原始网址：http://www.bioinformatics.org/JaMBW//main.html

软件名称：DNA Tool 6.0.122

软件大小：6.5M

简介：DNATool是一个功能很全面的DNA序列分析工具包，共享软件，可免费注册。包括的功能有：序列编辑与类似序列查找、建立自己的序列数据库进行查找、多序列比较、序列翻译、蛋白序列分析、引物设计与分析、基因表达序列分析（SAGE）功能等。它还包括DNA分析中常用到的一些功能，如碱基百分组成、分子量计算等，可以说包括了大多数DNA分析的功能，是一个不可多得的好工具。

原始网址：http://www.crc.dk/dnatools/

软件名称：pDRAW32 1.1.60

软件大小：2.6M

简介：一个非常方便的质粒绘制工具与DNA分析工具。它包括DNA序列输入与分析、限制酶消化分析以及环形与线性DNA图形输出等诸多功能。作者将许多选择设计成选项，只须你选择即可，使用非常简便。软件需要限制性酶数据库的支持。

原始网址：http://hjem.get2net.dk/acaclone/

软件名称：AnnHyb 4.b22

软件大小：1.1M

简介：DNA工具软件，它可以对短DNA序列进行补体序列生成、融合温度预测、GC百分含量计算、分子量计算、摩尔消光系数计算等功能。并新增了许多功能，包括序列检索、注释、编辑、格式转换、限制酶分析、翻译、序列查找、反序与补序、序列统计、ORF查找、寡序列分析、探针分析等等，是一个非常有用、简洁方便的小工具。

原始网址：http://bioinformatics.org/annhyb/

软件名称：DNAProbe

软件大小：116k

简介：一个很小但十分有用的DNA编辑软件。在确定蛋白家族新成员的基因序列过程中，常常需要根据蛋白质序列对比设计核苷酸序列，这种情况下，您就需要DNAProbe的帮助！
         To isolate genes for new members of a protein family, it is frequently necessary to design oligonucleotides on the basis of protein alignments.DNAPROBE assists in the design of oligonucleotides in such cases. Ituses MSF protein alignments generated by the program PILEUP and codon frequency tables from the Wisconsin (GCG) sequence analysis software package. The basic algorithm calculates the most probable nucleotide sequence corresponding to the alignment by summing the products of the frequency with which a particular amino acid occurs at any one position and the codon usage frequency for that amino acid. Where an alignment contains a cluster of closely related sequences, the user may choose to implement a weighting option that reduces their individual contributions
to the output in order that they do not overwhelm the contributions of more distantly related sequences which are under-represented. This may be done in two ways; (a) using the algorithm of Gerstein et al. (J.Mol. Biol., 236, 1067-1078) and the information contained in the dendrogram file written by PILEUP, or (b) by specifying weights in a separate file which is then read by the program, an option which enables one to give increased weight to sequences known to be more closely related to the target organism.

原始网址：http://www.simtel.net/product.download.mirrors.php?id=11651

软件名称：DNASP 4.10.9

软件大小：4.5M

简介：基因多态性分析软件，输入比对后的DNA序列文件，可进行基因多态性分析。
       
      DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. DnaSP can also carry out several tests of neutrality: Hudson, Kreitman and Aguadé (1987), Tajima (1989), McDonald and Kreitman (1991), Fu and Li (1993), and Fu (1997) tests. Additionally, DnaSP can estimate the confidence intervals of some test-statistics by the coalescent. The results of the analyses are displayed on tabular and graphic form.

View Data display：

 
 
Example of the output produced by DnaSP ：

 
 

原始网址：http://www.ub.es/dnasp/

软件名称：DNA FOR Windows 2.21

软件大小：704k

简介：一个易于使用的DNA分析软件，主要用于小规模的序列分析，如编辑与显示ABI仪器获得的色普文件。软件还有DNA翻译、限制性酶分析等功能，并可利用外部程序CLUSTALW等进行序列比对。

    DNA for Windows is a compact, easy to use DNA analysis program, ideal for small-scale sequencing projects.  It is particularly suited to working with chromatogram files from ABI machines, and is one of the few programs able to edit as well as view these files.  The program has powerful DNA translation and restriction enzyme analysis facilities, and works with external programs to produce multiple alignments and contigs with ease.

Figure 1.  Main application with list of  sequences (top window) text-based analysis (middle window) and graphical analysis (bottom window)

General Features：

  Three-window view - maximise one or view all three, making navigation easy.   Loads FASTA format sequences and extracts sequences from text files.
  Easy manipulation of sequences - removal of 'junk' text, reverse, complement, trim, etc.
  Restriction enzyme analysis - custom groups of enzymes, only show enzymes that cut a certainnumber of times.
  Translation of DNA to protein - Choice of 1-, 3- or 6-frame; can calculate mass of selected protein.
  Easy multiple sequence alignment using interface to CLUSTALW program.
  Manual multiple alignment - e.g. for 'tweaking' alignments.
  Calculation of codon usage.
  Automatic contig assembly - using interface to CAP program.
  Dot-Plot analysis of 1 or 2 sequences.
 

ABI Chromatogram Manipulation:

  Reads AND WRITES ABI chromatogram files.
  Views chromatogram, with scalable X- and Y- axes (see figure 2), custom colours, etc.
  Easy editing of base calls, with a single mouse click.
  Automatic alignment with a second chromatogram - to quickly check base calls, or assemble contig.
  Highly configurable printing of chromatogram - auto scaling of peak heights, line thickness, number of rows, etc.

Figure 2.  Chromatogram view window.

原始网址：http://www.dna-software.co.uk/

软件名称：Sequencher 4.6

软件大小：9.8M

简介：非常强大的DNA分析工具，功能包括序列编辑、拼接，ORF分析，蛋白翻译，酶切位点作图，杂合子识别等功能。还有其他功能等待您的发现和介绍。

The Variance Table – A powerful tool for SNP analysis and more

Compare sequences or contig consensus sequences, one at a time, or in batches, to generate an interactive variance table. This table lets you sift through large quantities of data so you can quickly access the positions of greatest interest to you. Each cell in the Variance table is linked to its original data, so you can easily validate or edit each putative difference. A variety of export options let you take the results of your Sequencher analysis to other applications.

Multiple Contig Variance Table

Single Contig Variance Table

Enhanced Feature Handling – Import Genbank Features

We also added the attribute of Feature Keys to our features, so you can more easily manage feature styles. You may import Genbank Feature keys, or designate a key for your own features. The new Define Feature Key Default Style user preference lets you distinguish introns from exons and variants from sequencing errors.

Sequencher 4.6 gives you more confidence

Sequencher now displays confidence and summary confidence information in the Project window, the Sequence Editor, and the Sequence Get Info window, so you can better monitor the quality of your data.

Customize your workspace

You can define the default positions of your windows and Sequencher remembers your settings for format and consensus options.

• Use motifs to highlight sub-sequences that you define.
• Remember your ruler settings between sessions.
• Choose optimal window layouts for your working style and save them.
• Customize the display of your project window.

原始网址：http://www.genecodes.com/demos/