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

The only information we have are the frequencies of the alleles.

• each row represents the frequency of an allele at a single marker for all the observed taxonomy units (OTUs)
• The table must have a heading row representing OTUs
• first column: marker names
• second column: alleles
• following columns: allele frequencies

example (This frequency table has two markers, each of which has two alleles. Three OTUs have allele frequency for each allele at each marker):

Marker    Allele   OTU1   OTU2   OTU3
Marker1   A1       0.4    0.3    0.8
Marker1   A2       0.6    0.7    0.2
Marker2   B1       0.1    0.5    0.6
Marker2   B2       0.9    0.5    0.6

Distance in PowerMarker needs to be imported if you want to construct NJ/UPGMA tree from your own distance.

• same format as in PHYLIP
• distance matrix should be symmetric and zero-diagonal

example (from PHYLIP):

Alpha    0.0000 1.0000 2.0000 3.0000 3.0000
Beta     1.0000 0.0000 2.0000 3.0000 3.0000
Gamma    2.0000 2.0000 0.0000 3.0000 3.0000
Delta    3.0000 3.0000 3.0000 0.0000 1.0000
Epsilon  3.0000 3.0000 3.0000 1.0000 0.0000

Tree in PowerMarker can be imported from PHYLIP format text files

No specific format is required for the table except that it must be a valid table which means each row in the table has the same number of columns. Heading row can be provided or generated. The first column (column of row names) can also be generated if not provided. The easiest way to import a table from Excel is to select the table in Excel and copy the selected table to the clipboard and import Table in PowerMarker from the clipboard.

Dataset can be exported to a text file in five different formats:

• raw format
• table format
• STRUCTURE format
• NEXUS format
• Arlequin format

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