Differences

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--- powermarker [2007/12/10 10:05] – heidi
+++ powermarker [2008/07/22 13:31] (current) – external edit 127.0.0.1
@@ Line 26: / Line 26: @@
 ===== Input Files =====
 PowerMarker supports table-like data format directly.
 ==== Dataset format: ====
@@ Line 31: / Line 33: @@
   * 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
+  * Columns with same names will be combined (two columns of alleles for a single marker will be combined to one column of genotypes)
-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)
@@ Line 54: / Line 55: @@
 **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):
 <code>
-Sample   Trait1  Trait2  Marker1  Marker2  Marker3
+Sample    Trait1   Trait2   Marker1   Marker2   Marker3
-Sample1  +       3.1     0/0      12/14    A/A
+Sample1   +        3.1      0/0       12/14     A/A
-Sample1  ?       4.5     1/0      12/12    B/B
+Sample1   ?        4.5      1/0       12/12     B/B
-Sample2  -       3.3     0/1      13/14    A/B
+Sample2   -        3.3      0/1       13/14     A/B
-Sample2  -       2.0     1/1      14/14    A/A
+Sample2   -        2.0      1/1       14/14     A/A
 </code>
+==== frequency data: ====
+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):
+<code>
+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
+</code>
+==== distance data: ====
+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):
+<code>
+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
+</code>
+==== tree data: ====
+Tree in PowerMarker can be imported from [[PHYLIP]] format text files
+==== table data: ====
+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.
+===== Export dataset =====
+Dataset can be exported to a text file in five different formats:
+  * raw format
+  * table format
+  * [[STRUCTURE]] format
+  * [[NEXUS]] format
+  * [[Arlequin]] format
 ===== How to cite =====
 Citation information can be obtained by selecting Help | How To Cite PowerMarker in the PowerMarker program.