Dear list members Below, I've compiled a list of answers to my request for software that handles polyploid data along with available comments. I have not yet tested the software, so comments are taken from the answers I had. AUTOTET (Thrall & Young, 2000) For genetic diversity of autotetraploids PopGene 3.2 (Yeh et al., 1997) For genetic diversity of allotetraploids Arlequin (Excoffier, Laval & Schneider, 2005) Fst Spagedi (Hardy & Vekemans, 2002) Fst (Weir & Cockerham) Structure (Pritchard, Stephens & Donally, 2000) Clustering MalHapFreq (Hastings & Smith, 2008) ML estimates of allele frequencies Adegenet (Jombart, 2008) (R package) Data manipulation, multivariate analyses and per se F-stats Tetra/Tetrasat (Markwith, Stewart & Dyer, 2006) Allotetraploids Lamarc For polyploids with unknown haplotype phase Migrate-N Popdist 1.2.0 GenoType (Meirmans & Tenderen, 2004) GenoDive (Meirmans & Tenderen, 2004) AMOVA MLTR (Ritland, 2002) Inbreeding/outcrossing Anders S. Larsen Mimersgade 118, 5.tv. 2200 Copenhagen N Phone no. +4535854345 Mobile no. +4561334345 anderslarsen333@hotmail.com