PowerMarker
manual

Version 3.25 (released on 2/5/2006)
PowerMarker is a comprehensive set of statistical methods for genetic marker data analysis, designed especially for SSR/SNP data analysis. PowerMarker builds a powerful user interface around both new and traditional statistical methods for population genetic analysis. PowerMarker is also a 2D Viewer - which was used intensively for visualizing linkage disequilibria results.

• Windows 98 or above
• Microsoft .NET framework redistributable

• haploid/diploid
• Microsatellite
• SNP
• RFLP

PowerMarker supports table-like data format directly.

• each row represents all the genetic and trait information for a single assay/individual
• There can be any numbers of columns
• first row of the table must be a heading row representing the names of columns (each column falls into one of the four categories: marker, categorical, quantitative or exclude)
• Columns with same names will be combined (two columns of alleles for a single marker will be combined to one column of genotypes)
• Exclude columns will not be imported
• missing data: any nonempty string (as long as this string is consistent for all the columns of the same type)
• Linkage file: does not have a header row of marker names

Dataset consists of four components:

• Genotype information: a set of loci, each locus represents all the genetic information for a single genetic marker (genetic information can be a single allele for haplotype data or a genotype of two alleles for genotype data. A single marker column in the table will be converted to a single locus)
• Assay information: categorical or numeric traits for assays
• Hierarchy: up to three levels of population structure
• Marker information: mapping information or other marker properties

There may be up to three hierarchical columns, which are special categorical columns (None of these three columns are required. If not defined, the hierarchical columns will be automatically generated):

• level-1 column: the column of assay IDs and it must be unique for each assay
• level-2 column: usually represents a population or a sample
• level-3 column: representing groups or superpopulations

example (includes three marker columns, two categorical columns (Sample and Trait2) and one numeric column (Trait1). The sample column can be set as a level-2 column):

Sample   Trait1  Trait2  Marker1  Marker2  Marker3
Sample1  +       3.1     0/0      12/14    A/A
Sample1  ?       4.5     1/0      12/12    B/B
Sample2  -       3.3     0/1      13/14    A/B
Sample2  -       2.0     1/1      14/14    A/A

Citation information can be obtained by selecting Help | How To Cite PowerMarker in the PowerMarker program.