Differences

This shows you the differences between two versions of the page.

--- immanc [2008/06/16 15:08] – created heidi
+++ immanc [2011/07/07 12:59] (current) – heidi
@@ Line 1: / Line 1: @@
 ====== Immanc (BayesAss) ======
-**[[http://rannala.org/moin.cgi/Software|Immanc / BayesAss]]**\\
+**[[http://www.rannala.org/?page_id=13/ BayesAss]]**\\
-[[http://rannala.org/moin.cgi/BA2_Users_Guide|documentation]]
+[[http://rannala.org/docs/BayesAss.1.3.pdf|documentation]]
 \\
-Immanc: Version 5.0 (8 Oct 1998)\\
+**Immanc:** Version 5.0 (8 Oct 1998)\\
 Detecting Immigrants Using Multilocus Genotypes.
 \\
-BayesAss+: Version 1.3 (Date 4 May 2005)\\
+**BayesAss+:** Version 1.3 (Date 4 May 2005)\\
 Bayesian Estimation of Recent Migration Rates Using Multilocus Genotypes.
 \\
-BayesAss: Version 2.0 (not released yet)\\
+**BayesAss:** Version 2.0 (not released yet)\\
 BayesAss is a program that estimates recent migration rates between populations using MCMC.  It also estimates each individual’s immigrant ancestry, the generation in which immigration occurred (i.e. the individual can be assigned as an immigrant from a specific population, a non-immigrant, or the offspring of an immigrant and a non-immigrant), the population (as opposed to the sample) allele frequencies, inbreeding (F) values within each population, and genotypes at any locus with missing data.
@@ Line 21: / Line 21: @@
   * Linux
   * Mac OSX
@@ Line 29: / Line 31: @@
   * RFLPs
   * SNPs
+  * Standard
   * allozymes
@@ Line 34: / Line 37: @@
 ===== Input Files =====
   * suffix of ''.inp'' or ''.txt''
-  * Two file formats are currently accepted by BayesAss: Structure format and Immanc format
+  * Two file formats are currently accepted by BayesAss: [[Structure]] format and Immanc format
 ==== Structure format ====
@@ Line 85: / Line 89: @@
 The setup for the data file should be:
 <code>
-Individual1	population1	locus1	allele1	allele2
+Individual1	population1	locus1	allele1	 allele2
-Individual2	population1	locus1	allele1	allele2
+Individual2	population1	locus1	allele1	 allele2
 </code>
@@ Line 126: / Line 130: @@
 ===== How to cite =====
-  * Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood Computer Applications in BioSciences 13:555-556.
+  * **BayesAss+:** G.A. Wilson and B. Rannala 2003. Bayesian inference of recent migration rates using multilocus genotypes. Genetics 163: 1177-1191.
-  * Yang, Z. 2007. PAML 4: a program package for phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution 24: 1586-1591 (http://abacus.gene.ucl.ac.uk/software/paml.html).
+  * **Immanc:** Rannala, B., and J.L., Mountain. 1997. Detecting immigration by using multilocus genotypes. Proceedings of the National Academy of Sciences USA 94: 9197-9201.