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Matthew Stephens - PHASE software for haplotype estimationPHASE: A system for rebuilding haplotypes from population data Most recent version info:The almost all recent edition of PHASE is v2.1.1, which featuresimproved combining for larger data units likened with v2.1,as properly as perfoming somé (very) rudimentarychecking óf the input file file format. (For several data units v2.1 andv2.1.1 will provide very equivalent solutions, but for somé datasets the results from v2.1.1 can become considerably better.)The most recent major release was v2.1, whichintroduced moreflexible versions for recombination (including recombination hotspots)and fixed a couple of bugs in v2.0.2.Description PHASE v 2.1 will be a system applying the method for reconstructing haplotypesfrom populace data, described in1 Stephens, Michael., Smith, In., and Donnelly, P. (2001).American Record of Human Genetics, 68, 978-989.2 Stephens, Meters., and Donnelly, G. (2003).American Diary of Individual Genetics, 73:1162-1169.3 Stephens, Michael., and Scheet, P. (2005).Us Journal of Human Genetics, 76:449-462.The software also incorporates strategies forestimating recombination prices, and identifying recombination hotspots,as explained in3 Li, In., and Stephens, M. Genetics, 165:2213-2233.4 Crawford et al (2004).
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Character Genetics, 36: 700-706.How to refer to this softwarePlease see user instructions for how to cite the software program.In all situations, please state the version of the software program used, and anydeviations fróm the default choices.Software program downloadPHASE is usually available under the following open source.I deliver executables of edition 2.1.1 for Linux and MicrosoftWindows. Contributed executables may be available for other platforms(find below). Resource program code (M) can be also available (below) for thosewho wish to compile it on some other operating techniques. If you perform manage tocompile the system effectively on another platform, and want tocontribute an executabIe for others tó use, please e-mail me theexecutable, ánd I will include it to this website.Executables fór v2.1.1.Linux (version 2.1.1) (put together with g):Toinstall the software program on a Linux system, download thé Linux executableby cIicking on the link above, and unzip it and untar it by keying$ gunzip phase.2.1.linux.tar.gz$ tar -xvf phase.2.1.1.linux.tarThis will generate a brand-new directory, stage.2.1.1.linux. Modification to thatdirectory, and look at the file instruct2.1.pdf for furtherinstructions.Microsoft Windows (version 2.1.1). (created with MinGW):Savé this executable file in a appropriate location on your computer (eg byright-cIicking on the link above).
You will also need to download the'supplementary documents' below - especially the guidelines! To runthe program you will require to open an MS-DOS windowpane (eg chooséStart-Run from thé begin menus, and after that type COMMAND in the promptand strike Okay).
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