phylogenetic analysis: 2.5 millions SNPs in 33 samples?

Question

[sun.nation]

I have huge SNP data set from 33 samples. Any suggestion of software to do phylogenetic tree analysis. I tried MEGA6 and it crashed several times. Thanks

Answer 1

[SNPsaurus]

How about RAxML? http://sco.h-its.org/exelixis/software.html

It has handled much larger populations on a small server, so may work for your needs.