% mafft --retree 0 --treeout --reorder --localpair --weighti 0 --minimumlinkage input
Newick tree
Reordered sequences
Size = 1000 sequences × 60-696 sites
Distance measure = score of pairwise global alignment
Clustering method = minimum linkage
MAFFT home:
http://mafft.cbrc.jp/alignment/software/
Archaeopteryx home:
https://sites.google.com/site/cmzmasek/home/software/archaeopteryx
Archaeopteryx references:
Zmasek and Eddy (2001)
Han and Zmasek (2009)