1.2 Weighted neighbor joining Bruno, Halpern, Socci W. J. Bruno, N. D. Socci, and A. L. Halpern. Weighted Neighbor Joining: A Likelihood-Based Approach to Distance-Based Phylogeny Reconstruction, Mol. Biol. Evol. 17 (1): 189-197 (2000). phylogeny weighbor infile Distances matrix File (-i) perl " -i $value" 1 phylip_dist perl 1 length Length of the sequences (-L) perl ($value)? " -L $value" : "" 2 Default is 500. This is the effective sequence length equal to the number of varying sites. Note if the -L option is not used then the program will print a warning message to stderr indicating that it is using this default length. size Size of the alphabet (-b) perl ($value && $value != $vdef)? " -b $value" : "" 4 2 Sets the size of the alphabet of characters (number of bases) b. 1/b is equal to the probablity that there will be a match for infinite evolution time. The default value for b is 4. Verbose output Verbose (-v) v verbose vv very verbose vvv very very verbose perl ($value)? " -$value" : "" 2 outfile perl " -o treefile" 3 treefile treefile phylip_tree perl 1