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baps [2008/06/16 10:50] – heidibaps [2013/02/20 13:24] (current) – heidi
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-Version 5.1\\+Version 5.4 (29.04.2010)\\
 A program for Bayesian inference of the genetic structure in a population. Assigns individuals to genetic clusters by either considering them as immigrants (mixture analysis) or ad descendants from immigrants (admixture analysis). A program for Bayesian inference of the genetic structure in a population. Assigns individuals to genetic clusters by either considering them as immigrants (mixture analysis) or ad descendants from immigrants (admixture analysis).
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 ===== Program information ===== ===== Program information =====
-  * Windows XP/2000/Vista +  * Windows XP/Vista/7 (32-bit, 64-bit) 
-  * Mac OS X +  * Mac Snow leopard OS X (64-bit) 
-  * Linux+  * Linux (32-bit) 
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 ===== Data type handled ===== ===== Data type handled =====
   * haploid/diploid/(tetraploid)   * haploid/diploid/(tetraploid)
-  * SNP+  * DNA 
 +  * SNP (sequence/numeric)
   * AFLP   * AFLP
   * Microsatellite   * Microsatellite
-  * multi-allelic markers+  * Standard (multi-allelic markers)
  
  
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 ==== Spatial clustering: ==== ==== Spatial clustering: ====
 Same as the first two above, except for the coordinate values that need to be given in a separate file: Same as the first two above, except for the coordinate values that need to be given in a separate file:
-  * as many rows as there are individuals (spatial clustering of individuals) or groups (spatial clustering of groups) in the molecular data set.+  * as many rows as there are individuals (spatial clustering of individuals -> sampling coordinates of each individual) or groups (spatial clustering of groups -> sampling coordinates of each group) in the molecular data set.
   * missing coordinate: two consecutive zeros   * missing coordinate: two consecutive zeros
  
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 **example:** **example:**
-  * Data flie: see first two example +  * Data file: see first example 
-  * Coordinate file: (sampling coordinates of each group or each ind -> clustering of groups of ind or clustering of ind)<code>+  * Coordinate file: <code>
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 155  96 155  96
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-=== BASP data format: ===+=== BAPS data format: ===
   * haploid marker data (single data row per individual)   * haploid marker data (single data row per individual)
   * diploid marker data (two rows per individual)   * diploid marker data (two rows per individual)
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 ===== How to cite ===== ===== How to cite =====
 +Tang J, Hanage WP, Fraser C, Corander J. (2009). Identifying currents in the gene pool for bacterial populations using an integrative approach. PLoS Computational Biology, 5(8): e1000455.
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 Corander, J., Waldmann, P., Marttinen, P. and Sillanpää, M.J. (2004).  BAPS 2: enhanced possibilities for the analysis of genetic population structure, Bioinformatics,  20, 2363-2369. Corander, J., Waldmann, P., Marttinen, P. and Sillanpää, M.J. (2004).  BAPS 2: enhanced possibilities for the analysis of genetic population structure, Bioinformatics,  20, 2363-2369.
  
baps.1213606257.txt.gz · Last modified: 2008/07/22 13:30 (external edit)