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