Data Format for Haploid organism

[Sajed]

Hi all

Can anyone suggest me in preparing the right data format/input file,
and in explaning about structring population using Haploid DNA. I am
going to analyze bacteria population using miscosatellite markers. I
have two big test population with different subpopulation.

Thanks and regards,

Sajed

[Mike]

Structure is really designed for genotypic data. You could use
Arlequin to measure differentiation/distance between
bacterial populations based on proportions of shared haplotypes (using
Reynolds or Slatkin's linearized Fst distances).
Arlequin will also let you perform an analysis of molecular variance
(AMOVA), which will allow you to determine whether the
diversity is partioned within or between populations/subpopulations.
AMOVA was initially developed specifically for haplotype data (mtDNA).

Arlequin web site: http://anthro.unige.ch/software/arlequin/

A good overview of AMOVA: http://www.bioss.ac.uk/smart/unix/mamova/slides/frames.htm

The first description of AMOVA:
L. Excoffier, P. E. Smouse, and J. M. Quattro.
Analysis of molecular variance inferred from metric distances among
DNA haplotypes: application to human mitochondrial DNA restriction
data.
Genetics, 131(2):479-491, 1992.

Hope that helps!

-Mike

[Jorge]

Sajed,
I have used structure for microsatellite data from a haploid organism.
For the file, just keep the data in columns. That is one column per
locus. Then in structure write 1 in diploidy. As for population
differentiation, I have used Arlequin it work fine, but you have to
diploidize your data (i.e. make each locus two columns), just keep
that in mind for other analyses. GenAlex 6.3 has an statistics
(Phist) similar to Fst that work just fine and you do not have to deal
with diploidization.
Jorge