HICKORY

version 1.1
Software for analysis of geographic structure in genetic data. The software implements the Bayesian method described in Holsinger (1999) for estimating F-statistics co-dominant marker data and the method described in Holsinger et al. (2002) for estimating F-statistics from dominant marker data. It also includes routines to allow posterior comparisons as described in Holsinger and Wallace (2004).

• Windows
• Linux

• dominant markers
• co-dominant markers

files in NEXUS format.

• need only an alleles block:

  #nexus
  begin alleles; [comments are surrounded by square brackets]
   dimensions newpops npops=2 nloci=3;
   format labels missing=? separator=/;
   locusallelelabels
    1 ’pgi 1’,
    2 ’pgi 2’,
    3 adh;
   matrix
    Embudo:
     indiv_1 A/A 100/110 slow/fast
     indiv_2 A/A 75 / 90 slow/slow
     indiv_3 A/a 75/100 fast/slow
     indiv_4 A/A 100/100 fast/fast,
    Black_Mesa:
     1 a/a 110/100 fast/slow
     2 a/A 75/100 slow/slow
     3 a/a 100/100 fast/fast
    ;
  end;

  • dimensions command:
    • nloci: number of loci scored
    • npops: number of populations scored
  • matrix command:
    • The genotype for a diploid locus at a co-dominant locus takes the form A/a
    • forward slash (/) symbol serves as a separator symbol, making it clear which pairs of alleles belong to each locus
    • If the loci represent dominant genetic markers, do not use the slash and specify only one allele for each locus
    • phenotype for a dominant locus:

• the hickory block is optional