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.
PowerMarker supports table-like data format directly.
Dataset consists of four components:
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):
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.
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.
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:
Citation information can be obtained by selecting Help | How To Cite PowerMarker in the PowerMarker program.