The function ResolveNames interacts with the TNRS server at iPlant that uses fuzzy name matching to find standardized taxonomic plant names. GetPhylotasticToken is similar, but can be used for animal taxa as well, since it also utilizes the NCBI and ITIS databases. GetPhylotasticToken returns a unique token that can be checked online or using the RetrieveTNRSNames function. CompareTNRS will compare the original list of names to the returned TNRS names to see which names changed.
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. See http://meta.microbesonline.org/fasttree/
MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two. The manual is also available here: http://www.drive5.com/muscle/manual/
WRAPPER DEPRECATED – one can install mafft on Agave API and use this wrapper as a prototype – MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of about 200 sequences), FFT-NS-2 (fast; for alignment of about 10,000 sequences), etc. See http://mafft.cbrc.jp/alignment/software/. The manual is also available here: http://mafft.cbrc.jp/alignment/software/manual/manual.html
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