PRANK is a command-line program that contains the latest features and the
complete set of options. It is ideal for scripting and non-interactive work,
and as it supports the MSAML-formatted output, the resulting alignments can
always be browsed using the graphical front-end in PRANKSTER

PRANK is developed on Linux but works also on MacOSX and Windows

Citation:
Loytynoja A, Goldman N. 2005. An algorithm for progressive multiple alignment
of sequences with insertions. PNAS 102:10557-10562