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Lines 1Īnd 2 give the haplotypes in the first individual, lines 3 and 4 give Each fileĬontains 100 data sets, one after each other with no blank lines.Įach dataset consists of Y lines. Number of haplotypes (=2*the number of individuals). X isĤNr where r is the recombination rate across the region, and Y is the truth.k1.t4.rX.Y: these files contain the "short sequence"ĭata simulated using Richard Hudson's program (from Figure 2).
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The archive contains files with names of the following forms: (If you are using UNIX you should be able to extract the files using unzip truthfiles.zip.) zip archive containing files of simulated data used for the manuscript by Stephens, Smith and Donnelly. Here is a text file of the results shown in Figures 2 and 3 in the paper. Who wish to do comparisons on the data sets used to The following resources are provided for the convenience of researchers Results and simulated data files from the paper Your computer by right-clicking on each of them, one at a time.) (You should be able to save these files on Supplied with other executables, so here they are for separateĭownload if you need them.
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See below for supplementary files and instructions in pdf format.Īll these files are supplied with the linux executable, but may not be Solaris (version 2.1.1) : (contributed by Frank Dudbridge) If you can't manage it, you may need to ask a resident Start-Run from the start menu, and then type COMMAND in the promptĪnd hit OK). The program you will need to open an MS-DOS window (eg choose "supplementary files" below - particularly the instructions! To run Save this executable file in a suitable place on your computer (eg by Change to thatĭirectory, and examine the file instruct2.1.pdf for further This will create a new directory, phase.2.1.1.linux.
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Install the software on a Linux system, download the Linux executableīy clicking on the link above, and unzip it and untar it by typing If you do manage toĬompile the program successfully on another platform, and wish toĬontribute an executable for others to use, please email me theĮxecutable, and I will add it to this website. Who wish to compile it on other operating systems.
Source code (C++) is also available (below) for those Contributed executables may be available for other platforms I distribute executables of version 2.1.1 for Linux and Microsoft PHASE is available under the following open source license. In all cases, please specify the version of the software used, and any
#PHASER 3.0 IS OUT HOW TO#
Please see user instructions for how to cite the software. Modelling Linkage Disequilibrium, and identifying recombination hotspots using SNP data Genetics, 165:2213-2233.Įvidence for substantial fine-scale variation in recombination The software also incorporates methods forĮstimating recombination rates, and identifying recombination hotspots, American Journal of Human Genetics, 76:449-462. American Journal of Human Genetics, 73:1162-1169.Īccounting for Decay of Linkage Disequilibrium in Haplotype Inference and Missing-Data Imputation. (2003).Ī comparison of Bayesian methods for haplotype reconstruction from population genotype data. American Journal of Human Genetics, 68, 978-989. (2001).Ī new statistical method for haplotype reconstruction from population data. Stephens, M., Smith, N., and Donnelly, P. The most recent major release was v2.1, whichįlexible models for recombination (including recombination hotspots)ĭescription PHASE v 2.1 is a program implementing the method for reconstructing haplotypes Sets the results from v2.1.1 can be considerably better.) V2.1.1 will give very similar answers, but for some data Improved mixing for larger data sets compared with v2.1,Īs well as perfoming some (very) rudimentaryĬhecking of the input file format. The most recent version of PHASE is v2.1.1, which features PHASE: A program for reconstructing haplotypes from population data Most recent version information: Matthew Stephens - PHASE software for haplotype estimation