PowerMarker

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https://www.researchgate.net/post/Could-anyone-recommend-the-best-software-for-genetic-diversity-and-population-structure-analysis
I have analyzed 16000 SNPs with GenALEx

Computer programs for population genetics data analysis: a survival guide Nature Reviews Genetics 7, 745-758 (October 2006) | doi:10.1038/nrg1904
http://www.nature.com/nrg/journal/v7/n10/abs/nrg1904.html

You can use the Popgene for genetic diversity and the Discriminant Analysis of Principal Component (DAPC) through the R package adegenet for population structure.

Arlequin, or DnaSP

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List of softwares used in molecular analysis:

Name

Description

Website

ARLEQUIN
An exploratory population genetics software environment able to handle large samples of molecular data (RFLPs, DNA sequences, microsatellites),

http://lgb.unige.ch/arlequin

POWER MARKER
Power Marker is a comprehensive set of statistical methods for genetic marker data analysis, designed especially for SSR/SNP data analysis.

http://www.powermarker.ne

MEGA5
Greatly facilitating a variety of different analyses.

http:/www.megasoftware.net

TFPGA
This program calculates descriptive statistics, genetic distances, and F-statistics. It also performs tests for Hardy-Weinberg equilibrium, exact tests for genetic differentiation, Mantel tests, and UPGMA cluster analyses.

http://www.marksgeneticsoftware.net/

GENEPOP
A population genetics software package

ftp://ftp.cefe.cnrs-mop.fr/pub/PC/MSDOS/GENEPOP/Genepop.zip also at http://wbiomed.curtin.edu.au/genepop/

NTSYSpc
Genetic diversity analysis software

http://www.exetersoftware.com/cat/ntsyspc/ntsyspc.html

STRUCTURE
Using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including microsatellites, RFLPs and SNPs.

http://pritch.bsd.uchicago.edu/

GENESTRUT
http://wwwvet.murdoch.edu.au/vetschl/imgad/GenStrut.htm

POPGENE
POPGENE is an R package that specifically focuses on statistical and population genetics methods.

http://www.ualberta.ca/~fyeh/index.htm

GRAPHICAL GENOTYPING PACKAGE (GGT)
GGT combines genetic map data and locus data to display Graphical Genotypes. Data can be viewed by individual or by linkage group, and sorted on markers.

http://www.dpw.wau.nl/pv/PUB/ggt/

G-MENDEL
A tool for construction of genetic linkage maps and analyzing Mendelian phenotypes.

http://cropandsoil.oregonstate.edu/G-mendel

JOINMAP
Construction of genetic linkage maps for several types of mapping populations: BC1, F2, RILs, (doubled) haploids, outbreeders full-sib family.. Everything available in an intuitive MS-Windows user interface.

http://www.joinmap.nl/

J/QTL
J/QTL is a Java GUI for the popular QTL data analysis software R/QTL. It provides a flexible and powerful working environment for users to perform a variety of tasks.

http://www.jax.org/staff/churchill/labsite/software/Jqtl/index.html

MANTEL-STRUCT
Tests for population structure through the use of Mantel tests

http://www.marksgeneticsoftware.net/

MAP MANAGER QT
A graphic, interactive program to map quantitative trait loci by regression methods; MAP MANAGER CLASSIC enhanced by quantitative trait mapping.

http://www.mapmanager.org/mmQT.html

MAPQTL
MultiQTL software integrates a broad spectrum of data mining, statistical analysis, interactive visualization and modeling tools that allow QTL analysis based on advanced and sophisticated methods for maximum extraction of the mapping information from data.

http://www.mapqtl.nl

MULTIMAP
Program for automated construction of genetic maps

http://compgen.rutgers.edu/multimap/multimapdist.html

MULTIMAPPER
Bayesian QTL mapping software for analysing backcross, double haploid, and F2 data from designed crossing experiments of inbred lines

http://www.rni.helsinki.fi/~mjs/

PROC QTL
PROC QTL is a user defined SAS procedure for mapping quantitative trait loci (QTL).

http://www.statgen.ucr.edu/software.html

QGENE
A free, computationally effecient, easy-to-use Java program for comparative analyses of QTL mapping data and population simulation.

http://coding.plantpath.ksu.edu/qgene/

QTL CARTOGRAPHER
A program to map quantitative traits sings a map of molecular markers.

http://statgen.ncsu.edu/qtlcart/cartographer.html

TASSEL
TASSEL is a software package which performs a variety of genetic analyses. The analyses include association mapping, diversity estimation and calculating linkage disequilibrium.

http://sourceforge.net/projects/tassel/

R/QTL
Program for mapping quantitative trait loci in experimental crosses.

http://www.rqtl.org

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https://bioinformaticshome.com/tools/SNP-tools.html
SNP分析工具

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https://courses.washington.edu/fish543/Software.htm

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https://sniplay.southgreen.fr/cgi-bin/analysis_v3.cgi