Main Page - The GenGIS wiki. Show questions. Evolution and Genomics. Genomic analyses of non-model organisms with RAD-seq and Stacks Instructor: Julian Catchen Institute of Ecology and Evolution, University of Oregon Expected learning outcome The goal of this exercise is to familiarize students with the use of next generation sequence data produced from Reduced Representation Libraries (RRL) such as Restriction site associated (RAD) tags.
Students will learn how to: Biology Software List. R-statistics blog. CRAN: Contributed Documentation. Resources to help you learn and use R. Isolation by Distance Web Service - Raw Data (diploid genotypes) Common Concepts in Statistics [M.Tevfik DORAK] Data Analysis. Data Analysis (data sheet) 1) Score the individual genotypes 2) Calculate genotype frequencies 3) Calculate allele frequencies 4) Using the observed allele frequencies, calculate the genotype frequencies you would expect under Hardy-Weinberg equilibrium.
Toucan backup. MakeUseOf has featured a collection of backup software for Windows, Mac, and Linux.
When backing up to additional locations, you probably also want to secure your files to ensure your files stay safe, whether in Windows, Linux, online, etc. To combine it all, Toucan is a portable and open-source syncing utility that also backups up and encrypts your data. Sounds like a neat combination, right? You can download Toucan from PortableApps.com, home for popular portable apps, such as essential must-haves and games. The download file is about 3MB. The user interface is pretty straightforward, with the upper portion dedicated to rules and options, while in the lower portions, you can see the files and folders selected.
Save Recurring Jobs & Rules You can set names for rules to exclude files based on name or file size (for more, see below), that you can also use in addition to the different modes for each function (sync, backup, secure, etc.) Arlequin. News 03.02.2013 Release of new R functions for R package ver 3.01 here.
The zip file contains a directory called Rfunctions, which needs to replace the Rfunctions directory located in your Arlequin home directory. Kgtests. KGTESTS is a Microsoft Excel Program that I prepared, which implements the k and g tests to check for signatures of population expansion as described by Reich and Goldstein (1998) and Reich et al. (1999). 1) Reich, D.E., Feldman, M.W. and Goldstein, D.B. (1999) Statistical Properties of Two Tests that Use Multilocus Data Sets to Detect Population Expansions, Mol Biol Evol, 16, 453-466. 2) Reich, D.E. and Goldstein, D.B. (1998) Genetic evidence for a Paleolithic human population expansion in Africa, Proc Natl Acad Sci U S A, 95, 8119-8123.
The associated downloads are as follows and are available for download, free of charge, under a general open-license agreement. 1) The program file: 2) The read_me file: 3) The source code: DETSEL. Bayescan. BayeScan is a command line based open source software, published under the GNU General Public License as published by the Free Software Foundation.
BayeScan is coded using standard C++ and can be easily compiled under any system having a C++ compiler available using the “Makefile” provided along with the source code. Since version 2.1, BayeScan now uses OpenMP to implement parallel calculation on multicore CPUs, and you need to use a compiler supporting OpenMP. In Mac OS X 10.7 (Lion), compiling with the gcc version included with Xcode (gcc-4.2) leads to an error at runtime when using more than one thread ("Abort trap: 6"). This is apparently a bug in Lion with OpenMP that will certainly be solved in a future update.
In the meantime you can compile it using gcc 4.6 available here, as I did myself for the binary version provided. We provide command line executables ready to be used under Microsoft Windows, Apple Mac OS X (Intel processors), Linux 32bits and 64 bits. UC Davis Bodega Marine Laboratory. Executable application for determining relative discriminatory power among candidate genetic loci.
Download WHICHLOCI [zipped] Requirements: This program will run on legacy Windows operating systems 95, 98, 00 or NT (including Macintosh emulations of these operating systems) and has no specific hardware requirements. The astounding increase in amount of information yielded by highly polymorphic molecular marker types such as microsatellites has significantly increased resolving power for discrimination among closely related populations. This together with increased automation of techniques for resolving genetic variation results in an overall boon of new information. Individual based methods for assessing most likely population origin are among the innovative statistical techniques emerging to take advantage of this increased amount of information (Petkau et al. 1995; Waser and Strobeck 1998; Banks and Eichert 2000).
Theory and Program Outline. Whichloci. Microsatellite Tutorial. Microsatellites consist of short, tandem repeats of DNA sequence. The sequence C A G C A G C A G C A G is a tri-nucleotide microsatellite with the C A G repeated four times. Variation in the number of repeats in a microsatellite arises due to DNA-polymerase errors during the DNA replication process. Software for Population Genetic Analyses.