Differences

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--- hickory [2007/12/13 11:07] – heidi
+++ hickory [2008/07/22 13:31] (current) – external edit 127.0.0.1
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 ====== HICKORY ======
-**[[http://darwin.eeb.uconn.edu/hickory/hickory.html|HICKORY]]**
+{{hickory2.png?400}}\\
+**[[http://darwin.eeb.uconn.edu/hickory/hickory.html|HICKORY]]**\\
+[[http://darwin.eeb.uconn.edu/hickory/documentation/Hickory.pdf|documentation]]
 \\
@@ Line 9: / Line 11: @@
   * Windows
   * Linux
 ===== Data type handled =====
   * dominant markers
   * co-dominant markers
+  * AFLP (amplified fragment length polymorphism)
+  * RAPD (random amplified polymorphic DNA)
+  * multi-allelic markers
@@ Line 58: / Line 65: @@
         * dominant phenotype is scored as ''1'' (or ''+'') or ''0'' (''−'') (default)
         * Hickory accepts the following alternatives: <code>
-dominant;                     -> default
+dominant;                 -> default
-dominant all:1;               -> default
+dominant all:1;           -> default
-dominant all:0;               -> dominant phenotype at all loci scored as 0 (recessive = 1)
+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 three loci scored as 1 and at last two loci scored as 0
+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 three loci scored as 1 and at last two 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.