Immanc (BayesAss)

http://www.rannala.org/?page_id=13/ BayesAss
documentation

Immanc: Version 5.0 (8 Oct 1998)
Detecting Immigrants Using Multilocus Genotypes.

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 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.

• Windows
• Linux
• Mac OSX

• diploid data
• microsatellites
• RFLPs
• SNPs
• Standard
• allozymes

• suffix of .inp or .txt
• Two file formats are currently accepted by BayesAss: Structure format and Immanc 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!)

• 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 

• 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

• 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

• 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.