What it does
QuickTree is an efficient implementation of the Neighbor-Joining algorithm, capable of reconstructing phylogenies from huge alignments in time less than the age of the universe.
Input
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 can be supplied in various other formats (fasta, phylip, clustalw, pfam, psiblast, selex) and will be converted to Stockholm format with the esl-reformat program, which is part of the HMMer package (hmmer.org).
Output
Quicktree will output either a distance matrix (in PHYLIP format, square distance matrix) or a Newick tree.
File Formats
The distance matrix input should be in phylip format, it can be a square matrix or a lower triangle matrix. The distance matrix output by quicktree will be a square matrix.
Example square distance matrix in phylip format:
5 Alpha 0.000 1.000 2.000 3.000 3.000 Beta 1.000 0.000 2.000 3.000 3.000 Gamma 2.000 2.000 0.000 3.000 3.000 Delta 3.000 3.000 3.000 0.000 1.000 Epsilon 3.000 3.000 3.000 1.000 0.000
Example of a lower triangle matrix:
7 Mouse Bovine 1.7043 Lemur 2.0235 1.1901 Orang 2.0593 1.2005 1.5356 Gorilla 1.6664 1.3460 1.4577 1.5935 Chimp 1.7320 1.3757 1.7803 1.7119 1.0635 Human 1.7101 1.3956 1.6661 1.7599 1.0557 0.6933