This tool is based on EMBOSS command fneighbor that is a wrapper command for command neighbor of the PHYLIP package.
Phylogenies from distance matrix by N-J or UPGMA method is an implementation by Mary Kuhner and John Yamato of Saitou and Nei's "Neighbor Joining Method," and of the UPGMA (Average Linkage clustering) method. Neighbor Joining is a distance matrix method producing an unrooted tree without the assumption of a clock. UPGMA does assume a clock. The branch lengths are not optimized by the least squares criterion but the methods are very fast and thus can handle much larger data sets.
For more details, please check the manual page of fneighbor command.
Input is a phylip formatted distance matrix file.
Output consists of two files containing. One containing a human readable output report (neighbor.txt ) and a treefile (treefile.txt) that can be used as an input for tree drawing tools (Plot an unrooted tree, Plot cladogram).