| http://www.w3.org/ns/prov#value | - My usual routine to transform an alignment into a ML tree (I am mostly working on 16S rDNA, by the way) is to convert the sequences from fasta (I use mostly MUSCLE to align, and the wonderfully intuitive Se-Al to check my alignments) to nexus, load the sequences in PAUP* and fire up the ModelTest block until the best model is selected.
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