Analyses in SAMBAR https://github.com/mennodejong1986/SambaR.git
Once imported the dataset, SNPs have to be filtered using command 
filterdata(indmiss=0.5,snpmiss=0.05) #to generate dataset A, Dataset A excluded samples with more than 50% missing data and all loci with greater than 5% missing data. 
filterdata(indmiss=0.25,snpmiss=0.05) #to generate dataset B.Dataset B excluded samples with more than 25% missing data and all loci with greater than 5% missing data

NOTE: most of the following commands can be found with SambaR manual https://github.com/mennodejong1986/SambaR/blob/master/sambaR_manual.docx

To preform structure analyses as PCoA and LEA and f3 run
findstructure()

TO EXTRACT INPUT FILE FOR ALL OTHER ANALYSES 
Run the command in SambaR
esportsambarfiles()

INPUT FILES FOR ARLEQUIN TO PERFORM FST
use PGD Spider (link for download http://www.oracle.com/technetwork/java/javase/downloads/index.html) to convert ped file in .arp file  
now you can use .arp file in Arlequin (link for download http://cmpg.unibe.ch/software/arlequin35/win/WinArl35.zip ) to perform Fst 

INPUT FILE FOR BAYESASS 
generated with exportsambarfiles() 
In a Unix environment, run the software Bayesass :
BA3-SNPS-Ubuntu64 --file Bayesassinput.immanc.txt --loci XXXXX -u -t -s 10 -i 1000000 -b 100000

TO RUN ADMIXTURE
use .ped file generated with exportsambarfiles() command
Use plink to convert the ped file into a bed file:
plink --file metapop.retainedinds.filter.number --allow-extra-chr --make-bed --recode A --out metapop.retainedinds.filter.number

In a Unix environment, run the software ADMIXTURE
for k=2
./admixture –cv metapop.retainedinds.filter.number.bed 2 –j4
for k=3 
./admixture –cv metapop.retainedinds.filter.number.bed 3 –j4
Note: at the end of the run you get cross validation error
The .Q file generated will be used to plot results (see https://dalexander.github.io/admixture/admixture-manual.pdf)

TREEMIX
The input file 'Treemixinput.snpsfilter.txt' was generated from autosomal data using the SambaR command:
exportsambarfiles()
The Treemix output files were generated using the commands:
gzip Treemixinput.snpsfilter.txt
In a Unix environment, run the software Treemix
/treemix -i Treemixinput.snpsfilter.txt.gz -bootstrap -k 500 -m 1 -root Atl -o replicate1

DEMOGRAPHY
SFS-vectors generated by ANGSD https://github.com/ANGSD/angsd.git for each dataset
In a Unix environment, run the software ANGSD
./angsd -out outFileName -bam bam.filelist -GL 1 -doMaf 1 -doMajorMinor 1 -nThreads 10
Once you have SFS, in a Unix environment, rub the software stairwayplot https://github.com/xiaoming-liu/stairway-plot-v2.git
open the file two-epoch_fold.blueprint’ and edit as suggested in the manual https://github.com/xiaoming-liu/stairway-plot-v2/raw/master/READMEv2.1.pdf
then run the following command:
java -cp stairway_plot_es Stairbuilder mypop.blueprint &  
and 
bash mypop.blueprint.sh &