hickory
This is an old revision of the document!
Table of Contents
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).
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:
#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
- 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+
) or0
(−
) (default) - Hickory accepts the following alternatives:
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
- 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.
hickory.1197541533.txt.gz · Last modified: 2008/07/22 13:30 (external edit)