Tools
I have previously used and warmly recommend the following, not exhaustive list of applications for your analyses:
Important tools for Data Science:
My commonly used bionformatics tools:
Population Genetics Tools:
ARLEQUIN (AMOVA, Fstats) http://cmpg.unibe.ch/software/arlequin35/
STRUCTURE (Admixture, Pop structure) http://pritch.bsd.uchicago.edu/structure.html
GÉNÉTIX (FCA, Fstats) http://kimura.univ-montp2.fr/genetix/
TCS (Networks) http://darwin.uvigo.es/software/tcs.html
NewHybrids (Hybrid Detection) http://ib.berkeley.edu/labs/slatkin/eriq/software/software.htm#NewHybs
Populations (Pop trees) http://www.bioinformatics.org/~tryphon/populations/
EasyPop (Simulations) http://www.unil.ch/dee/page36926_fr.html
All-purpose tools:
MEGA (free) http://www.megasoftware.net/
CLC Genomic Workbench (commercial) http://www.clcbio.com/index.php?id=28
Nice tutorials and webinars:
PGAP Prokaryotic Annotation Tool https://www.youtube.com/watch?v=pNn_-_46lpI