## Phylogenies from distance matrix by N-J or UPGMA method

### Description

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.

### Parameters

- Type of data matrix (fneighbor parameter -matrixtype )
- Neighbor-joining or UPGMA tree (fneighbor parameter -treetype )
- Species number to use as outgroup (fneighbor parameter -outgrno )
- Randomise input order of species (fneighbor parameter -jumble )
- Random number seed between 1 and 32767 (must be odd\) (fneighbor parameter -seed )
- Subreplicates (fneighbor parameter -replicates)
- Write out trees to tree file (fneighbor parameter -trout )
- Print data at start of run (fneighbor parameter -printdata )
- Print out tree (fneighbor parameter -treeprint )
- Collect a log file

For more details, please check the manual page of fneighbor command.

### Input and output

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).