The selection choice offered for tools and analyses is based on the Datatype and Ntaxa and Dataset Format in your uploaded file:
Currently, we accept NEXUS, PHYLIP, HENNIG86 formatted files. FASTA file is also accepted for Multiple Sequence Alignment - CLUSTALW.

	DNA_DATATYPE	RNA_DATATYPE	AA_DATATYPE	ALL OTHERS
ML GTR+I+G	GARLI	GARLI
ML GTR+G	RAxML Rec-I-DCM3(RAxML)(for ntaxa >= 500) GARLI	RAxML Rec-I-DCM3(RAxML)(for ntaxa >= 500) GARLI
WAG+Gamma+F			RAxML Rec-I-DCM3(RAxML)(for ntaxa >= 500)
MP	PAUP Rec-I-DCM3(PAUP)(for ntaxa >= 100)	PAUP Rec-I-DCM3(PAUP)(for ntaxa >= 100)	PAUP Rec-I-DCM3(PAUP)(for ntaxa >= 100)	PAUP Rec-I-DCM3(PAUP)(for ntaxa >= 100)
MSA	CLUSTALW(for FASTA dataset only)	CLUSTALW(for FASTA dataset only)	CLUSTALW(for FASTA dataset only)
BI	MrBayes		MrBayes
	ML = Maximum likelihood tree inference MP = Parsimony tree inference GTR+I+G = General time reversible model with Gamma-distributed among- site rate heterogeneity and invariant sites GTR+G = General time reversible model with Gamma-distributed among- site rate heterogeneity WAG+Gamma+F = WAG + Gamma + Empirical State Frequencies MSA = Multiple Sequence Alignment BI = Bayesian Inference