### THE PROGRAM PERMUT AND THE PROGRAM CpSSR BECOME ONLY ONE PROGRAM.

When you run the program you can choose if you want to use permut or CpSSR.

**README PERMUT**

This program is based on the papers (Pons & Petit Genetics 1996, 144:1237-1245) and (Burban et al. 1999, *Mol Ecol***8**, 1593-1602).

It computes measures of diversity and differenciation from haploid population genetic data, when a measure of the distance between haplotypes is available, and test whether the differentiation and diversity measures differ from the equivalent measures that do not take into account the distances between haplotypes (ie, that consider all haplotypes equally divergent).

The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:

First line :

Number of cytotypes Number of populations Number of characters distinguishing the variants (for instance number of polymorphic fragments, or of polymorphic nucleotide sites). The program asks for the number of permutations to be made.

see the example (\ExamplePermut\input.txt and \ExamplePermut\output.out).

Then follows the number of individuals having a given cytotype (column) in a given population (row). Finally, and without interruption, provide the table of character states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals!

The output file provides permutated values of Nst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Nst value is larger than the Gst, we count how many permutated values are larger than the observed Nst. If you have 5% of the permutated values greater than the observed value of Nst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Nst.

**README CpSSR** :

It computes measures of diversity and differenciation from haploid population genetic data, when the difference in number of repeats between alleles is available, and tests whether the differentiation and diversity measures differ from the equivalent measures when the distances between haplotypes is not considered (ie, when all haplotypes are considered equally divergent). The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:

First line :

Number of cytotypes Number of populations Number of cpSSR loci. The program asks for the number of permutations to be made. See the example (\ExampleCpSSR\input.txt and \ExamplePermut\CpSSR.out).

Then follows the number of individuals having a given haplotype (column) in a given population (row).

Finally, and without interruption, provide the table of length variant states for all haplotypes, where each line corresponds to one haplotype, and each column to a character.

No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals!

The output file provides permutated values of Rst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value

(by construction). To test if the observed Rst value is larger than the Gst, you count how many permutated values are larger than the observed Rst. If you have 5% of the permutated values greater than the observed value of Rst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Rst. I usually go for a one-sided test (i.e. I test if Rst>Gst, and not Rst<>Gst).

**VERSIONS**

*version 1.2.1: 2012-08-28

- Fix bug found by Jing Li
- Fix bug found by Ciara Lockstadt
- Fix bug found by Jianli

*Version 1.1: Fusion with CpSSR program. New choice: Weight distances between haplotypes by their frequencies or not.

*Version 1.0: 2005-04 No Parameters Limitation New Graphical Interface. Delphi Program.

*First Version; 2001-08-03 Parameters limitation size: the number of cytotypes is limited to 50, the number of populations is limited to 100, the number of populations is limited to 40 Turbo Pascal Program

**HELP**

For scientific problem: petit_at_pierroton.inra.fr

For thechnical problem: Frederic.Raspail_at_pierroton.inra.fr