Tree output format options

Three output formats are offered: 1) Clustal, 2) Phylip, 3) Just the distances.

None of these formats displays the results graphically. To see a graphic representation, get the PHYLIP package and use format 2) below. It can be imported into the PHYLIP programs RETREE, DRAWTREE and DRAWGRAM and displayed graphically.

1) Clustal format output. This format is verbose and lists all of the distances between the sequences and the number of alignment positions used for each. The tree is described at the end of the file. It lists the sequences that are joined at each alignment step and the branch lengths. After two sequences are joined, it is referred to later as a NODE. The number of a NODE is the number of the lowest sequence in that NODE.

2) Phylip format output. This format is the New Hampshire format, used by many phylogenetic analysis packages. It consists of a series of nested parentheses, describing the branching order, with the sequence names and branch lengths. It can be used by the RETREE, DRAWGRAM and DRAWTREE programs of the PHYLIP package to see the trees graphically. This is the same format used during multiple alignment for the guide trees.
Some other packages that can read and display New Hampshire format are TreeTool, TreeView, Phylowin and NJPlot.

3) The distances only. This format just outputs a matrix of all the pairwise distances in a format that can be used by the Phylip package. It used to be useful when one could not produce distances from protein sequences in the Phylip package but is now redundant (Protdist of Phylip 3.5 now does this).

4) TOGGLE PHYLIP BOOTSTRAP POSITIONS By default, the bootstrap values are placed on the nodes of the phylip format output tree. This is inaccurate as the bootstrap values should be associated with the tree branches and not the nodes. However, this format can be read and displayed by TreeTool, TreeView and Phylowin. An option is available to correctly place the bootstrap values on the branches with which they are associated.