Microsatellite Toolkit

The Excel add-in MS_tools.xla contains Microsoft Excel visual basic macros for use with diploid
or haploid microsatellite data. The macros run in Excel 97 or later for PC.
Use the Microsatellite tools to:

Check your data for errors

Create input files for population genetic analysis programs

Find duplicated or genetically identical samples

Calculate allele frequencies and diversity statistics

Data Format Requirements for Microsatellite Toolkit

Before starting, check that your data conforms to the format requirements:

Locus names should be in the first row of the worksheet

Sample names should be in the first column

The first allele should be in cell B2

Missing alleles data should be entered either as a blank cell or as zero ('0')

Samples in the same population should be grouped together

Sample names should consist of the population name and the sample number

(i.e. PopOne1, PopOne2, PopOne3 PopTwo1, PopTwo2, PopTwo3 )

There should be no gaps (blank rows) between populations

For diploid data, you can use either of two formats:

One-Column Diploid format
Two-Column Diploid format
For haploid data, there is only one format.
See examples, next page.
'One-column' diploid format:

B
1
locus1
2 Sample1 Allele1
3
Allele 2
4 Sample2 Allele1
5
Allele 2
6 Sample3 Allele1
7
Allele 2

C
locus2
Allele1
Allele 2
Allele1
Allele 2
Allele1
Allele 2

D
locus3
Allele1
Allele 2
Allele1
Allele 2
Allele1
Allele 2

Two-column diploid format:

A

B
1
locus1
2 Sample1 Allele1
3 Sample2 Allele1
4 Sample3 Allele1

D
locus2
Allele2 Allele1
Allele2 Allele1
Allele2 Allele1

F
locus3
Allele2 Allele1
Allele2 Allele1
Allele2 Allele1

G
Allele2
Allele2
Allele2

Haploid format:
A

B
1
locus1
2 Sample1 Allele1
3 Sample2 Allele1
4 Sample3 Allele1

C
locus2
Allele1
Allele1
Allele1

D
locus3
Allele1
Allele1
Allele1

Using MS Toolkit
1. Open the file containing your data and select the sheet with the data on it. Check that the data
complies with the data format requirements.
2. From the 'Tools' menu, select the 'Microsatellites' submenu, and click 'Microsatellite Toolkit'
(Keyboard shortcut Alt-t-r-m)
3. Data Settings
The data settings form is displayed. Select the correct format (diploid one- or two-column, or
haploid), and check that the number of samples and loci is correct - amend if necessary.
You can choose to check allele data for errors. If you do check your data, you can specify
maximum and minimum expected allele sizes, and the largest expected gap in allele size at any
locus.

4. Populations and Loci

Next, a form displaying the names of populations and loci detected is displayed. You can select
which populations and loci to use by double clicking them or selecting them and using the arrow
button to select / exclude them. (A list of populations and loci used will be included in the
output).
5. Output options
Next, a form giving various output options is displayed. You can choose to format your data for
various population genetics programs, to find matching samples or calculate allele frequencies
and diversity statistics.
For some options, such as input file formatting, you can decide to combine your populations into
a single population (for other options such as matching sample detection, this is not relevant).
Once you have selected the options you want, click GO!, and the program will do the
calculations and output results for each option to a new worksheet.
5. For saving input files for population genetics programs, select the relevant worksheet, and use
the 'Save sheet as textfile' option from the 'Microsatellites' submenu (Keyboard shortcut Alt-t-rt). Select the correct destination folder, and specify a valid name (make sure you use the correct
file extension, if required).