====== Immanc (BayesAss) ======
**[[http://www.rannala.org/?page_id=13/ BayesAss]]**\\
[[http://rannala.org/docs/BayesAss.1.3.pdf|documentation]]
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**Immanc:** Version 5.0 (8 Oct 1998)\\
Detecting Immigrants Using Multilocus Genotypes.
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**BayesAss+:** Version 1.3 (Date 4 May 2005)\\
Bayesian Estimation of Recent Migration Rates Using Multilocus Genotypes.
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**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.
===== Program information =====
* Windows
* Linux
* Mac OSX
===== Data type handled =====
* diploid data
* microsatellites
* RFLPs
* SNPs
* Standard
* allozymes
===== Input Files =====
* suffix of ''.inp'' or ''.txt''
* Two file formats are currently accepted by BayesAss: [[Structure]] format and Immanc format
==== Structure format ====
* first column: individual label
* the second: population label
* the remaining columns: the alleles
* labels:
* each label must be unique (either a unique individual or population)
* Alphabetical characters, strings, and (positive or negative) numbers may be used
* two rows are expected for each diploid individual (data must be diploid!)
=== example ===
* data for 10 individuals, with 5 individuals sampled from each of 2 populations, and each individual genotyped for 4 loci:
ind0 0 0 0 A 0
ind0 0 1 0 1 1
1.1 0 0 2 0 2
1.1 0 0 1 1 0
2 0 2 1 0 2
2 0 1 0 1 2
3 0 1 1 B 1
3 0 2 2 0 0
4 0 0 2 0 2
4 0 2 1 1 0
joe 1 0 1 0 1
joe 1 0 2 2 0
11 1 2 1 2 1
11 1 1 2 0 1
12 1 2 2 1 0
12 1 1 2 1 0
13 1 2 1 0 2
13 1 1 1 2 2
ann 1 1 1 1 0
ann 1 0 2 2 1
==== Immanc format ====
* Columns can be separated by any whitespace
* Missing genotypes should be represented by ''0'', ''00'', or ''000''
* Blanks are not allowed
* first column: individual label
* the second: population label
* the third: locus label
* the remaining 2 columns: the alleles at each locus that make up a genotype
* Spaces within names are not allowed
* each individual has a row entry for every locus
* the order of the alleles determines the haplotype phase (this information is not currently used and so the ordering is arbitrary)
* (ignore text after ''%'')
The setup for the data file should be:
Individual1 population1 locus1 allele1 allele2
Individual2 population1 locus1 allele1 allele2
=== example ===
* data for 15 individuals from two populations, genotyped for two loci:
ind1 pop1 locA 194 198
ind2 pop1 locA 198 198
ind3 pop1 locA 192 198
ind4 pop1 locA 190 198
ind5 pop1 locA 190 194
ind6 pop1 locA 194 198
ind7 pop1 locA 190 198
ind8 pop1 locA 184 190
ind9 pop1 locA 190 192
ind10 pop1 locA 184 192
ind11 pop2 locA 184 194
ind12 pop2 locA 190 194
ind13 pop2 locA 184 194
ind14 pop2 locA 192 194
ind15 pop2 locA 184 194
ind1 pop1 locB 158 162
ind2 pop1 locB 148 162
ind3 pop1 locB 150 158
ind4 pop1 locB 152 158
ind5 pop1 locB 162 162
ind6 pop1 locB 152 158
ind7 pop1 locB 152 156
ind8 pop1 locB 158 162
ind9 pop1 locB 162 162
ind10 pop1 locB 162 162
ind11 pop2 locB 162 162
ind12 pop2 locB 150 162
ind13 pop2 locB 158 162
ind14 pop2 locB 152 156
ind15 pop2 locB 156 158
===== How to cite =====
* **BayesAss+:** G.A. Wilson and B. Rannala 2003. Bayesian inference of recent migration rates using multilocus genotypes. Genetics 163: 1177-1191.
* **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.