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