Bioinformatics/popgen
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Evolution and Genomics | Stacks
Genomic analyses of non-model organisms with RAD-seq and Stacks Instructor: Julian Catchen
Common Concepts in Statistics [M.Tevfik DORAK]
Genetics Population Genetics Genetic Epidemiology Bias & Confounding Evolution HLA MHC Homepage M.Tevfik Dorak, MD, PhD Please use this address next time : http://www.dorak.info/mtd/glosstat.html
R
MakeUseOf has featured a collection of backup software for Windows , Mac , and Linux .
toucan backup
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 software package DetSel has been developed to identify markers that show deviation from neutral expectation in pairwise comparisons of diverging populations.
DETSEL
BayeScan is a command line based open source software, published under the GNU General Public License as published by the Free Software Foundation.
bayescan
Salmon Genetics Software | UC Davis Bodega Marine Laboratory
Executable application for determining relative discriminatory power among candidate genetic loci.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.
Microsatellite Tutorial
COALESCE : estimates the effective population size of a single constant population using nonrecombining sequences. DnaSP : estimates several measures of DNA sequence variation within and between populations, linkage disequilibrium, recombination, gene flow and gene conversion. FLUCTUATE : estimates the effective population size and an exponential growth rate of a single growing population using nonrecombining sequences. GENETREE : allows ancestral inference from DNA sequences from single or subdivided populations which conform to the infinite sites model. IM : Isolation Model testing- multiple versions w/ migration