hickory
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====== HICKORY ====== | ====== HICKORY ====== | ||
- | **[[http:// | + | {{hickory2.png? |
+ | **[[http:// | ||
+ | [[http:// | ||
+ | |||
+ | \\ | ||
+ | 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 ===== | ===== Program information ===== | ||
+ | * Windows | ||
+ | * Linux | ||
+ | |||
+ | |||
===== Data type handled ===== | ===== Data type handled ===== | ||
+ | * dominant markers | ||
+ | * co-dominant markers | ||
+ | * AFLP (amplified fragment length polymorphism) | ||
+ | * RAPD (random amplified polymorphic DNA) | ||
+ | * multi-allelic markers | ||
+ | |||
+ | |||
+ | |||
+ | |||
+ | |||
+ | |||
===== Input Files ===== | ===== Input Files ===== | ||
+ | files in [[NEXUS]] format | ||
+ | * need only an **alleles block:** < | ||
+ | #nexus | ||
+ | begin alleles; [comments are surrounded by square brackets] | ||
+ | | ||
+ | | ||
+ | | ||
+ | 1 ’pgi 1’, | ||
+ | 2 ’pgi 2’, | ||
+ | 3 adh; | ||
+ | | ||
+ | Embudo: | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | 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 phenotype is scored as '' | ||
+ | * Hickory accepts the following alternatives: | ||
+ | dominant; | ||
+ | dominant all: | ||
+ | dominant all: | ||
+ | dominant 1,2,3:1 4, | ||
+ | dominant 1-3:1 4-5: | ||
+ | </ | ||
+ | |||
+ | \\ | ||
+ | * the **hickory block** is optional: | ||
+ | * you can set parameters governing the MCMC sampler | ||
+ | |||
+ | |||
===== How to cite ===== | ===== How to cite ===== | ||
+ | * Holsinger, K. E. 1999. Analysis of genetic diversity in geographically structured populations: | ||
+ | * Holsinger, K. E., P. O. Lewis, and D. K. Dey. 2002. A Bayesian approach to inferring population structure from dominant markers. Molecular Ecology 11: | ||
+ | * 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.1197463829.txt.gz · Last modified: 2008/07/22 13:30 (external edit)