注册 登录  
 加关注
   显示下一条  |  关闭
温馨提示!由于新浪微博认证机制调整,您的新浪微博帐号绑定已过期,请重新绑定!立即重新绑定新浪微博》  |  关闭

wangyufeng的博客

祝愿BB 健康开心快乐每一天

 
 
 

日志

 
 

CLUMPP:a program that deals with label switching and multimodality problems in population-genetic cluster analyses.  

2012-12-07 22:59:59|  分类: 数量遗传学 |  标签: |举报 |字号 订阅

  下载LOFTER 我的照片书  |

CLUMPP is a program that deals with label switching and multimodality problems in population-genetic cluster analyses. CLUMPP permutes the clusters output by independent runs of clustering programs such as structure, so that they match up as closely as possible. The user has the option of choosing one of three algorithms for aligning replicates, with a tradeoff of speed and similarity to the optimal alignment. A program note describing CLUMPP was published in Bioinformatics 23: 1801-1806 (2007). [Example]

[Download software package (includes the manual)] (you will be directed first to a registration page and we would very much appreciate if you register)
       [Download manual]
       [Download software note (Bioinformatics 23: 1801-1806)]

To use the UNIX versions, unzip and untar the files in an appropriate directory using

gunzip filename.tar.gz; tar xvf filename.tar

where "filename.tar.gz" is the downloaded file. Winzip will unzip the Windows version. Run the program by typing

./CLUMPP

in UNIX or

CLUMPP

from a Dos prompt in Windows. It will permute the matrices in the input file to produce as close an alignment as possible.

Please send comments or problems with CLUMPP to Mattias Jakobsson.


Software history
June 18, 2010 - upload of version 1.1.2b software for windows
June 6, 2009 - upload of version 1.1.2 manual and software
October 10, 2007 - upload of version 1.1.1 manual and software
May 1, 2007 - upload of version 1.1 manual and software
December 22, 2006 - upload of version 1.0 manual and software

CLUMPP:a program that deals with label switching and multimodality problems in population-genetic cluster analyses. - 喜欢吃桃子 - wangyufeng的博客

 

These graphs show the estimated population structure (plotted using distruct) for 10 runs of structure using 1056 individuals from 52 human populations. Each graph represents the output of one run of structure. In each graph, each individual is represented by a vertical line, which is partitioned into 5 colors that represent its estimated membership fractions in K=5 clusters. Black vertical lines separate the individuals from different populations. The 10 runs shown are the 10 runs with K=5 that are described in Figure 1 of Science 298: 2381-2385 (2002).

In the pre-CLUMPP figure, the distruct plots are made directly from the structure output. In the post-CLUMPP figure, CLUMPP has been used to permute the 10 runs so that the clusters align across runs. To make the figure, the Greedy algorithm of CLUMPP was used with 10,000 random input orders of runs. The plot shown represents the optimal alignment among the 10,000 input orders tested.

  评论这张
 
阅读(1352)| 评论(0)
推荐 转载

历史上的今天

在LOFTER的更多文章

评论

<#--最新日志,群博日志--> <#--推荐日志--> <#--引用记录--> <#--博主推荐--> <#--随机阅读--> <#--首页推荐--> <#--历史上的今天--> <#--被推荐日志--> <#--上一篇,下一篇--> <#-- 热度 --> <#-- 网易新闻广告 --> <#--右边模块结构--> <#--评论模块结构--> <#--引用模块结构--> <#--博主发起的投票-->
 
 
 
 
 
 
 
 
 
 
 
 
 
 

页脚

网易公司版权所有 ©1997-2017