Data Analysis †

Arrangement of Data Sequence Scanner Software v1.0 https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600583&tab=Overview The free Sequence Scanner Software enables you to view, edit, print and export sequence data generated using the Applied Biosystems Genetic Analyzers. The software generates graphically expressive reports on results.

MEGA4 http://www.megasoftware.net/ MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.

Peak Scanner™ Software v1.0 https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=603624 Use this free software to perform DNA fragment analysis; separate a mixture of DNA fragments according to their sizes, provide a profile of the separation, and precisely calculate the sizes of the fragments. The software allows you to view, edit, analyze, print, and export fragment analysis data generated using the Applied Biosystems Genetic Analyzers.

Notepad++ http://notepad-plus.sourceforge.net/uk/site.htm Notepad++ is a free (as in "free speech" and also as in "free beer") source code editor and Notepad replacement that supports several languages. Running in the MS Windows environment, its use is governed by GPL License.

Software of Population genetics Arlequin ver 3.11 http://cmpg.unibe.ch/software/arlequin3/ The goal of Arlequin is to provide the average user in population genetics with quite a large set of basic methods and statistical tests, in order to extract information on genetic and demographic features of a collection of population samples.

Genepop 4.0 http://kimura.univ-montp2.fr/~rousset/Genepop.htm Genepop implements a mixture of traditional methods and some more focused developments: It computes exact tests for Hardy-Weinberg equilibrium, for population differentiation and for genotypic disequilibrium among pairs of loci; It computes estimates of F-statistics, null allele frequencies, allele size based statistics for microsatellites, etc., and of number of immigrants by Barton & Slatkin's 1986 private allele method; It performs analyses of isolation by distance from pairwise comparisons of individuals or population samples, including con_dence intervals for “neighborhood size". Genepop converts data from the Genepop input format to formats of some softwares that were around in Genepop's youth; there was little need to update this option as many more recent softwares for population genetic analyses read input _les in the Genepop format.

FSTAT ver. 2.9.3 http://www2.unil.ch/popgen/softwares/fstat.htm FSTAT is a computer package for PCs which estimates and tests gene diversities and differentiation statistics from codominant genetic markers. It computes both Nei and Weir & Cockerham families of estimators of gene diversities and F-statistics, and tests them using randomisation methods.

GenAlEx ver. 6.1 http://www.anu.edu.au/BoZo/GenAlEx/ GenAlEx is a user-friendly cross-platform package for population genetic analysis that runs within Microsoft Excel(TM). GenAlEx enables population genetic data analysis of codominant, haploid and binary genetic data providing analysis tools applicable to plants, animals and microorganisms.

CONVERT http://www.agriculture.purdue.edu/fnr/html/faculty/rhodes/students%20and%20staff/glaubitz/software.htm CONVERT is a user-friendly, 32-bit Windows program that facilitates ready transfer of co-dominant, diploid genotypic data amongst commonly used population genetic software packages. CONVERT reads input files in its own ‘standard' data format, easily produced from an Excel file of diploid, co-dominant marker data, and can convert these to the input formats of the following programs: GDA, GENEPOP, ARLEQUIN, POPGENE, MICROSAT, PHYLIP, and STRUCTURE. CONVERT can also read input files in GENEPOP format. In addition, CONVERT can produce a summary table of allele frequencies in which private alleles and the sample sizes at each locus are indicated.