====== HICKORY ======
{{hickory2.png?400}}\\
**[[http://darwin.eeb.uconn.edu/hickory/hickory.html|HICKORY]]**\\
[[http://darwin.eeb.uconn.edu/hickory/documentation/Hickory.pdf|documentation]]

\\
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).

===== Program information =====
  * Windows
  * Linux


===== Data type handled =====
  * dominant markers
  * co-dominant markers
  * AFLP (amplified fragment length polymorphism)
  * RAPD (random amplified polymorphic DNA)
  * multi-allelic markers






===== Input Files =====
files in [[NEXUS]] format
  * need only an **alleles block:** <code>
#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;
</code>
    * **dimensions command:** 
      * nloci: number of loci scored
      * npops: number of populations scored
    * **format command:**
      * missing: character to be used for missing data (missing diploid genotype would thus be specified as ?/?)
    * **locusallelelabels command:**
      * optional (loci will simply be numbered)
      * comma-separated list of locus number and locus name pairs
    * **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 (dominant marker): 
        * keyword ''dominant''
        * dominant phenotype is scored as ''1'' (or ''+'') or ''0'' (''−'') (default)
        * Hickory accepts the following alternatives: <code>
dominant;                 -> default         
dominant all:1;           -> default
dominant all:0;           -> dominant phenotype at all loci scored as 0 (recessive = 1) 
dominant 1,2,3:1 4,5:0;   -> dominant phenotype at first 3 loci scored as 1 and at last 2 loci scored as 0
dominant 1-3:1 4-5:0;     -> dominant phenotype at first 3 loci scored as 1 and at last 2 loci scored as 0
</code>

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  * the **hickory block** is optional:
    * you can set parameters governing the MCMC sampler


===== How to cite =====
  * Holsinger, K. E. 1999. Analysis of genetic diversity in geographically structured populations: a Bayesian perspective. Hereditas 130:245-255.
  * Holsinger, K. E., P. O. Lewis, and D. K. Dey. 2002. A Bayesian approach to inferring population structure from dominant markers. Molecular Ecology 11:1157-1164.
  * Holsinger, K. E., and L. E. Wallace. 2004. Bayesian approaches for the analysis of population structure: an example from Platanthera leucophaea (Orchidaceae). Molecular Ecology 13:887-894.
  * Song, S., D. K. Dey, and K. E. Holsinger. 2006. Differentiation among populations with migration, mutation, and drift: implications for genetic inference. Evolution 60:1-12.