/ 
bioperl-1.2.2
/ Bio::Tools::Phylo::Molphy::Result

NAME

Bio::Tools::Phylo::Molphy::Result - DESCRIPTION of Object

SYNOPSIS

Give standard usage here

DESCRIPTION

Describe the object here

FEEDBACK

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Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web:

bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/

AUTHOR - Jason Stajich

Email jason@bioperl.org

Describe contact details here

CONTRIBUTORS

Additional contributors names and emails here

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

Title   : new
Usage   : my $obj = new Bio::Tools::Phylo::Molphy::Result();
Function: Builds a new Bio::Tools::Phylo::Molphy::Result object 
Returns : Bio::Tools::Phylo::Molphy::Result
Args    :

model

Title   : model
Usage   : $obj->model($newval)
Function: 
Returns : value of model
Args    : newvalue (optional)

substitution_matrix

Title   : substitution_matrix
Usage   : my $smat = $result->subsitution_matrix;
Function: Get the relative substitution matrix calculated in the ML procedure
Returns : reference to hash of hashes where key is the aa/nt name and value
          is another hash ref which contains keys for all the aa/nt 
          possibilities
Args    : none

transition_probability_matrix

Title   : transition_probability_matrix
Usage   : my $matrixref = $molphy->transition_probablity_matrix();
Function: Gets the observed transition probability matrix
Returns : hash of hashes of aa/nt transition to each other aa/nt 
Args    : none

residue_frequencies

Title   : residue_frequencies
Usage   : my %data = $molphy->residue_frequencies()
Function: Get the modeled and expected frequencies for
          each of the residues in the sequence
Returns : hash of either aa (protml) or nt (nucml) frequencies
          each key will point to an array reference where
          1st slot is model's expected frequency
          2nd slot is observed frequency in the data
          $hash{'A'}->[0] = 
Args    : none

next_tree

Title   : next_tree
Usage   : my $tree = $factory->next_tree;
Function: Get the next tree from the factory
Returns : L<Bio::Tree::TreeI>
Args    : none

rewind_tree

Title   : rewind_tree_iterator
Usage   : $result->rewind_tree()
Function: Rewinds the tree iterator so that next_tree can be 
          called again from the beginning
Returns : none
Args    : none

add_tree

Title   : add_tree
Usage   : $result->add_tree($tree);
Function: Adds a tree 
Returns : integer which is the number of trees stored
Args    : L<Bio::Tree::TreeI>

search_space

Title   : search_space
Usage   : $obj->search_space($newval)
Function: 
Returns : value of search_space
Args    : newvalue (optional)