QuickTree is an efficient implementation of the Neighbor-Joining algorithm (PMID: 3447015), capable of reconstructing phylogenies from huge alignments in time less than the age of the universe.
QuickTree is written in ANSI C and should complile and run on a number of different platforms. "make quicktree" from this directory should compile the program and place the executable in the current directory.
quicktree -h gives a list of options.
QuickTree accepts both distance matrix and multiple-sequence-aligment inputs. The former should be in PHYLIP format. The latter should be in Stockholm format, which is the native alignment format for the Pfam database. Alignments in various formats can be converted to Stockholm format with the sreformat program, which is part of the HMMer package (hmmer.org).
The tress are written to stdout, in the Newick/New-Hampshire format use by PHYLIP and many other programs.
Any problems, please contact klh@ebi.ac.uk
Kevin Howe, 2002