================================================================================== 1. Phylogenetic Tree HOWT - Introduction o Querying and manipulating phylogenetic tree once they have been created.

o Data captured objets are Trees and their Nodes o A Tree is made of nodes and relationships that connect these nodes. o The basic respresntaion of parent and child nodes is intended to represent the directionality of evolution. - Major objects or modules o Bio:: Tree::Tree Major Tree object Main entry point to the data represented by a tree Container for some summary information about the tree and a desecription of the trees root node. o Bio::Tree::Node Major Node Object. Node representator. A Node can only have 1 parent and it can have 1 or many children - Simple usage o Tree are used to represent the history of a collection of taxa, sequences, or populations. - Reading and writing trees o Bio::TreeIO=== Bio::Tree::Tree Driver Modules Formate Comments Bio::TreeIO::newick New Hampshire or Reading &writing Newick formate Bio::TreeIO::nhx New Hampshire Reading & writing eXtended formate Bio:TreeIO::nexus PAUPs Nexus formate Reading & prasing nto writing

Example code Use Bio::TreeIO; # parse in newick/new Hampshire formate My $input = new Bio::TreeIO (-file => tree.tre -formate => newick my $tree = $input ->next_tree; Bio::Tree::TreeImethods #Request the taxa (leaves of the tree). My @taxa =$tree->get_leaf_nodes; My$root=$tree->get_rood_node;

# Total length of the tree my $total_length = $tree->total_branch_length; Bio::TreeFuncitonsI

Advanced Topics:-generating Random Tree Topologies

2. Bio::Tools::phylo::PAML HOWTO - Introduction

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Running PAML from within Bioperl

Accessing paml results Running PAML from within Bioperl