This program accepts a wide range on input format. Included NBRF/PIR, FASTA, EMBL/Swissprot, Clustal, GCC/MSF, GCG9 RSF and GDE.
The output format can be one or many of the following: Clustal, NBRF/PIR, GCG/MSF, PHYLIP, GDE, NEXUS.
These are done automatically when you select "Do Complete Alignment". Other options are "Do Alignment from guide tree" and "Produce guide tree only".
Pairwise alignments are computed for all against all sequences, and similarities are stored in a matrix. This is then converted into a distance matrix, where the distance measures reflect the evolutionary distance between each pair of sequences.
From this distance matrix, a guide tree, or phylogenetic tree, for the order in which pairs of sequences are to be aligned and combined with previous alignments is constructed using a neighbour-joining clustering algorithm. Sequences are progressively aligned at each branch point, starting from the least distant pair of sequences.
The main parameters are the gap opening penalty, and the gap extension penalty.