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Usage: quicktree [-options] <inputfile>
Options:
-in <m|a>        : input file is a distance matrix in phylip format (m)
                   or an alignment in stockholm format* (a, default)
-out <m|t>       : output is a distance matrix in phylip format (m) or
                   a tree in New Hampshire format

Advanced options :
-upgma           : Use the UPGMA method to construct the tree
                     (ignored for distance matrix outputs)
-kimura          : Use the kimura translation for pairwise distances
                     (ignored for distance matrix inputs)
-boot <n>        : Calcuate bootstrap values with n iterations
                     (ignored for distance matrix outputs)

*Use sreformat, part of the HMMer package to convert your alignment to Stockholm format