With concatenated SNPs, tree generation needs to include correction for ascertainment bias - not available in fasttree. Tree generation now done (v1beta.3) using RAxML v 8.1+ which allows for ascertainment bias correction (uses the ASC_ prefix for the model: i.e. -m ASC_GTRGAMMA). Uses fast raxml tree generation option (-f a), so is definitely NOT exhaustive!
With concatenated SNPs, tree generation needs to include correction for ascertainment bias - not available in fasttree. Tree generation now done (v1beta.3) using RAxML v 8.1+ which allows for ascertainment bias correction (uses the ASC_ prefix for the model: i.e. -m ASC_GTRGAMMA). Uses fast raxml tree generation option (-f a), so is definitely NOT exhaustive!