software introduction on DNA

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I will introduce some softwares on DNA
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$ w0 V$ N; Q/ x$ Q1 i* m4 I+ M1 jambw 1.10 X* ?0 N$ z6 p7 d" Z8 i2 `  B
软件大小： 1,900K
& Z. i9 H+ X, N) m9 Q/ S软件语言： 英文 ) {; [5 v" ^3 T, b' i. T9 c
软件类别： DNA分析类
5 R  T! C( c, N# B运行环境： Win9x/Me/NT/2000/XP/2003 . ^  c3 w+ h, {- J4 T5 N
加入时间： 2009-7-142 w& C7 r8 m5 T
原始网站： Home Page # N- y1 x# V; s6 s
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JaMBW, the Java based Molecular Biologist's Workbench5 c/ v. d. l8 _6 ^
The programs and documentation that you will find hereby enclosed had been put together in order to try to give a free access to the exploitment of the most common bioinformatic operations that a molecular biologist currently has. The peculiar aspect of JaMBW, however, is to take advantage of the foremost developments in computer science in order to deliver information in a way simple to use. The latter includes, therefore, point-and-click, drag-and-drop, plug-and-play. Most of these requirements are met by the use of Java programming language conformant to the JDK1.02 specifications. To the user of these resources, however, the implementation details are of null interest.& P+ b. Z' w7 T% F

/ j8 t0 C7 Y% A# b9 i- r) v; f+ RJava语言是一个跨操作平台的语言，用该语言编写的软件，可以跨操作平台使用，只要这个系统有支持Java语言的环境即可。在Windows环境下，IE与Netscape 浏览器均支持Java 语言，所以用 Java语言编写的分子生物学软件JaMBW便是在浏览器下工作的。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。JaMBW是一个非常出色的工具软件。版本号1.1。* r# w6 ^( _+ N4 v9 G$ d! x
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2 ChromasPro 1.50. I1 K6 o* _* p; A
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软件大小： 886K
4 c8 |0 V9 Y0 I, c7 `% y% L软件语言： 英文
3 w  f0 o$ d1 R* u软件类别： DNA分析类
7 w. e+ a+ N" \5 q运行环境： Win9x/Me/NT/2000/XP/2003 8 D  ], F1 i4 w8 x
加入时间： 2009-7-14
3 H$ A  q  e) g" w( I9 r" y7 P$ [原始网站： Home Page
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* Opens chromatogram files from Applied Biosystems and Amersham MegaBace DNA sequencers.- P8 R* J& K1 I& I7 V( y( V
* Opens SCF format chromatogram files created by ALF, Li-Cor, Visible Genetics OpenGene, Beckman CEQ 2000XL and CEQ 8000, and other sequencers./ D+ A' N7 G3 @+ v3 C0 ]% j' H
* View Genescan genotype files.
$ u# M* R' Q* i+ s( p$ d) G9 _* Save in SCF or Applied Biosystems format.
6 ~* [; z# c& E" l9 a: F* Prints chromatogram with options to zoom or fit to one page." _1 n& J4 z/ L' X6 S7 J0 R
* Exports sequences in plaint text, formatted with base numbering, FASTA, EMBL, GenBank or GCG formats.( \2 c9 j; ]2 |0 t
* Copy the sequence to the clipboard in plain text or FASTA format for pasting into other applications.
/ i$ |  a6 q- m) ]' J  t* Export sequences from batches of chromatogram files, with automatic removal of vector sequence.
2 U7 j6 w' E" W( `8 n* Reverse & complement the sequence and chromatogram.1 }, T; E- e! \- A+ A8 w) K' X
* Search for sequences by exact matching or optimal alignment.
  a& d3 y, d' S) W5 P* Display translations in 3 frames along with the sequence.
5 E( B5 m/ P/ T# `" [: t9 y* Copy an image of a chromatogram section for pasting into documents or presentations.0 A# V# R( y( q. [- w
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一个可打开ABI格式序列文件，查看与编辑的Windows95软件。原始网站有Windows3.1版本。 共享软件，可免费使用60天,lite版本为免费版。注册费$240。
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3 AnnHyb v.4.942
: \5 _, l' _, q. }5 ^4 ~软件大小： 1,292K2 ?9 E- @8 }- }8 W  L9 y% z
软件语言： 英文 0 X( K8 A& h- o
软件类别： DNA分析类% v$ G% T( w& j5 {) P0 s
运行环境： Win9x/Me/NT/2000/XP/2003
. p4 P5 U; s  J) Q4 ~) m2 q加入时间： 2009-7-147 R8 y6 x8 g4 X8 H
原始网站： Home Page
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AnnHyb is a tool for working with and managing nucleotide sequences in multiple formats.
  L7 C. }- `* nThe features include format conversion, sequence viewer, sequence editor, oligonucleotides alignment, restriction analysis, pattern searching, retrieval from servers, multi-alignment viewer, consensus determination ...6 s4 h7 U, b  u; |2 |- c1 X! I  h

  ^( G& \% o0 R& c3 U+ Q) l: j5 KDNA工具软件，对短DNA序列，它可进行补体序列生成、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。增加了许多功能，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，是一个有用而方便的小工具。
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4 DnaSP 5.00.07
* y4 H# b: }$ ^: R7 Z) B  |6 J软件大小： 4,749K
  d/ L: Y/ O( F' ^0 q% u软件语言： 英文
$ h! H$ o$ ?) R软件类别： DNA分析类
3 B3 E* o1 o0 m& C5 {: a/ E运行环境： Win9x/Me/NT/2000/XP/2003
% m; \7 \4 n. G! p- f- {& W加入时间： 2009-7-15
% O2 Z5 M" H" B( b. s原始网站： Home Page) g" x+ j) w: t- Z9 N

; {7 k* T' w- J9 T0 ^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.
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5 DFW 2.51 trail7 f3 F$ u% G5 P* w4 g; d' E. Z5 I. d
软件大小： 704K
( E; U: f8 m7 j9 C- T7 i5 i1 P软件语言： 英文 # L0 m# ?2 D4 {( [3 a
软件类别： DNA分析类
! e4 v, Q" y, v+ i* y运行环境： Win9x/Me/NT/2000/XP/2003
% o' B: S4 E1 k7 t" A  E加入时间： 2007-10-21
8 R( x9 ~" l3 X& y原始网站： Home Page   Y6 j/ H7 S% ^3 E# M

  _# t4 P; y+ L  U  }1 }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.
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+ o  @6 V' L& `; t; P* i/ ~DNA for Windows的缩写，是一个易于使用的DNA分析软件，主要用于小规模序列分析，例如用来编辑与显示ABI仪器获得的色谱文件。程序具有DNA翻译与限制酶分析功能，并可以利用外部程序CLUSTALW 进行序列比对。注册费50英镑。
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6 Artemis R11
" }/ H$ C) \, f6 L4 l3 W# ?/ T, P6 _软件大小： 7,803K* ]* T/ X  d/ e( c. R
软件语言： 英文
9 A' c9 ~" o* k# e* U) K软件类别： DNA分析类  O0 S. ~2 t; M- l2 e; a
运行环境： Win9x/Me/NT/2000/XP/2003 ) H, i5 C9 q0 V7 B2 I
加入时间： 2009-4-25
" h1 G* u( O9 F原始网站： Home Page ; \- ?2 F' U$ ]+ D% y

3 P+ ?8 x. @6 w7 c  X# HArtemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. Artemis is written in Java, and is available for UNIX, GNU/Linux, BSD, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK database entries or sequence in FASTA or raw format. Extra sequence features can be in EMBL, GENBANK or GFF format. 8 j/ W6 v0 ?) O7 l3 }

5 O& g2 J0 J9 J& \( K3 nArtemis是a DNA sequence viewer and annotation tool的缩写，为一个免费的DNA序列查看器与注释工具，可以以图形形式查看序列的各种分析结果与特性。以Java写成，需要安装JRE1.2后(5.1M)，直接双击便可执行。程序读取EMBL与GENBANK格式的序列与纯DNA序列，为英国桑格中心推出。使用手册，1M。- h) `( d% ^, h$ O; ]

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7 ACT R8- e$ j* ?: n" z2 d* t3 I
软件大小： 7,803K+ ?5 N1 n+ X/ ~: P
软件语言： 英文
2 Q6 I% j1 R8 C3 `: G软件类别： DNA分析类( i0 F  ]) w8 ?4 |+ {$ U
运行环境： Win9x/Me/NT/2000/XP/2003
4 V! h! b2 Y2 H9 P加入时间： 2009-4-257 J3 r) ^0 T& L" L$ z
原始网站： Home Page
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" Z7 C$ x9 f! K( F' CACT (Artemis Comparison Tool) is a DNA sequence comparison viewer based on Artemis. In common with Artemis, ACT is written in Java and runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK entries or sequence in FASTA or raw format. Extra sequence features can be in EMBL, GENBANK or GFF format.
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是Artemis Comparison Tool的缩写，DNA序列比较查看器，基于Artemis程序写成，也是以Java语言推出，需要安装JRE1.2后(5.1M)，直接双击便可执行。。主要用来读取与显示blastx与tblastx的比较结果，也可以读取与图形化查看EMBL与GENBANK数据库的条目，同样为英国桑格中心推出。使用手册，880K。5 ~: o/ T9 L* \; g5 u9 o0 r& I
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8 GDA 1.1( c/ t5 U6 U6 Q* {2 N
软件大小： 733K7 y" a9 y* _2 X! X( a, u; R/ H0 N
软件语言： 英文 5 c/ E9 [  L% c, V
软件类别： DNA分析类" S" }/ Q, i- L( ~" z: m  J4 I
运行环境： Win9x/Me/NT/2000/XP/2003
$ M2 y6 X2 _6 B) Z* E7 ?4 [2 U加入时间： 2008-6-144 K8 N; [0 g5 p8 ]; u/ _7 w/ o' a/ Y
原始网站： Home Page , d) \; Y; i, J! d' l1 ?

* E2 B: D  L9 O% g% n2 a! FProgram by Paul O. Lewis and Dmitri Zaykin designed to accompany the book "Genetic Data Analysis" by Bruce S. Weir (1996, Sinaur Associates). Computes linkage and hardy-weinberg disequilibrium, some genetic distances, and provides method-of-moments estimators for hierarchical F-statistics.# Y3 w: R7 d. K; B- h; u1 A& D6 n

- N- \  @: o# j. U5 [+ g/ n5 uChris Basten has compiled a command-line-only version of GDA that runs under Mac OS 10.2.8 and 10.3 (Jaguar and Panther). This version can be downloaded here. After downloading, you should open a terminal window, navigate to the folder containing the file, and type "chmod +x gda1.1" to make GDA executable.% y3 L: q! a! p

& J; n- H4 }6 d! fGDA为(Genetic Data Analysis)的缩写，主要用来进行不连续基因数据的统计分析，输入文件格式为NEXUS ，BIOSYS ,Weir与GeneStrut 。
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9 Sequencher 4.9 Demo
3 @, m* I( `: D/ U2 [# d. G软件大小： 45,000K* X7 H, p) y2 }
软件语言： 英文
( E+ V5 W9 n3 I: H% G; M软件类别： DNA分析类0 ~& Q9 U( ~( {0 e
运行环境： Win9x/Me/NT/2000/XP/2003
& q5 z0 ~: D+ [( S, \% C加入时间： 2009-4-27
2 j4 g4 C/ M: c: P* `原始网站： Home Page
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Sequencher is the industry standard software for DNA sequence analysis. It works with all automated sequencers and is widely known for its lightning-fast contig assembly, short learning curve, user-friendly editing tools, and superb technical support. First released almost 15 years ago, Sequencher is currently used for sequence analysis tasks in every major genomic and pharmaceutical company as well as numerous academic and government labs in over 40 countries around the world. Life Science researchers use Sequencher for many diverse DNA sequence analysis applications including de novo gene sequencing, mutation detection, forensic human identification, systematics, and more.
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4 \2 q$ M0 i8 B5 |7 O6 x' Y1 {序列拼接软件，还具有ORF分析、蛋白翻译、酶切位点作图、杂合子识别等分析功能。价格单机版3350美元。/ t/ O  g+ \' W& |
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Lasergene and vectorNTI