Tools to Support Phylogenetic Analysis

Introduction

Over the coming year FIG and its friends plan on developing and releasing a number of tools to support phylogenetic analysis. At this point, we are making available a tool for inserting taxa into a tree, assuming that one has an alignment of SSU rRNA and a tree that includes some subset of the taxa in the alignment. At one time this technology was used to extend the tree distributed by thye Ribosomal Database Project. We have revived it and make it available now as a first step in supporting the development of a large SSU-based phylogenetic tree. By itself, it is not adequate for many tasks. A few key tools are needed to complement the set we are making available. We plan on making these additional tools available over the coming year.

Extending an Existine Tree by Insertion of One Sequence at a Time

Assuming that you have
  1. a new alignment (call it ssu_alignment.fasta),
  2. a table giving a correspondence between IDs and organisms (call it ssu.names), and
  3. an old tree (call it old.ssu.tree).
you should follow these steps to extend the tree:
You can display your tree (very crudely) using
	display_tree new.ssu.tree ssu.names
Note that the tree is unrooted. We supply a command for rooting it, but you do need to understand exactly where you wish to place the root. To root it, use
	root_at Node1 Node2 FractionBetween < UntootedTree > RootedTree
where the the nodes are specified as either
  1. tip id, or
  2. three ids separated by commas (which gives a unique point in the tree).

You can extract a representative tree by using
	representative_tree big.tree N 
where big.tree is the file containing a newick tree and N is the number of nodes desired in the representative tree.