counthaplotype
PURPOSE 
COUNTHAPLOTYPE - Counts haplotypes
SYNOPSIS
function [numHap,sizHap,seqHap] = counthaplotype(aln)
DESCRIPTION
CROSS-REFERENCE INFORMATION
This function calls:
This function is called by:
- DsDn DSDN - Estimates Ds and Dn
- PsPn PSPN - Estimates Ps and Pn
- fu97Fs FU97FS - Compute Fu's Fs statistic
- hapdiv HAPDIV - Haplotype diversity/heterozygosity (hd)
- snp_ehh SNP_EHH - Extended Haplotype Homozygosity of phased haplotype data
- snp_freqpie SNP_FREQPIE - Pie chart of allele and genotype frequencies among populations
- snp_genopct SNP_GENOPCT - percentage of valid genotype data
- snp_hapfreqem SNP_HAPFREQEM - EM algorithm to estimate probabilities of haplotypes
- snp_obshet SNP_OBSHET - observed percentage of heterozygosity indiv
- thetaewen THETA_EWEN - Estimates theta (4N*mu) using formula 9.26 in Ewens' book
- wall99bq WALL99BQ - Wall's B & Q statistic test
- watterson78f WATTERSON78W - Watterson's homozygosity test of neutrality (1978)
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