fdist2
Table of Contents
FDist2 (datacal)
A program to detect loci that might be under selection in samples from structured populations.
Program information
- Linux
- DOS
Data type handled
- Microsat
- DNA
- Standard (multi-allelic marker)
Input Files
fdist2 - this is the simulation program:
- consists of 6 lines:
- Total number of demes (100 max)
- No of populations sampled (must be less than or equal to total number of demes)
- Expected Fst for infinite allele, infinite island model
- Sample size (assumed the same in all populations)
- Indicator - 1 for stepwise mutations; 0 for infinite alleles
- No of realizations (loci)
example
100 15 0.17 50 0 20000
datacal
- 1/0 indicator: alleles by rows in data matrix (1), or pops by rows (0).
- No of pops
- no of loci
- no of alleles at locus 1
- matrix of data at locus 1 either with each row corresponding to the same allele or to the same population
- no of alleles at locus 2
- matrix…
- etc.
- The data matrices can contain populations for which a locus was not genotyped, these should be indicated by zero entries
example
0 15 2 3 4 76 0 45 115 0 109 11 0 120 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 67 0 47 65 0 0 0 0 0 0 0 0 74 6 7 64 9 26 74 0 3 4 23 53 0 38 122 0 72 48 0 57 63 0 0 0 0 0 0 0 0 0 0 0 0 0 0 80 0 0 112 0 0 0 0 0 0 0 0 80 0 8 72 0 16 84
How to cite
- Beaumont and Nichols. Evaluating loci for use in the genetic analysis of population structure. (1996) Proc Roy. Soc. Lond. B. 263: 1619-1626
- Flint et al. Minisatellite mutational processes reduce F-st estimates. (1999) Human Genet 105: 567-576
fdist2.txt · Last modified: 2011/06/10 11:23 by heidi