[Bioperl-l] Find distances between LCA's and the other nodes from a tree

Ross KK Leung ross at cuhk.edu.hk
Mon Oct 3 06:28:38 EDT 2011


Dave wrote:

>You can read more about this here: http://www.bioperl.org/wiki/Advanced_BioPerl#Bioperl_Interface_design

Thanks for this reference, it is very good for me to understand better the architecture of Bioperl.

 

>So, if I understand your question correctly, you should be able to use all of the NodeI methods l on the LCA nodes. However, and here's where I'm a bit confused, is_monophyletic is something you'd call on a Tree object, not on a Node object, right?

But the following codes will generate errors because lca cannot be identified.

 

my $treein = Bio::TreeIO->new( -file => $testtree, -format => 'newick' );
while( my $tree = $treein->next_tree ){

       my @leaves = $tree->get_leaf_nodes;

       foreach my $leaf1( @leaves ){

               my $id1 = $leaf1->id;

               foreach my $leaf2( @leaves ){

                       my $id2 = $leaf2->id;

                          my $distance = $tree->distance( -nodes => [$leaf1,$leaf2] );



                       if ($id1 eq "A" and $id2 eq "B") {
                               my $lca = $tree->get_lca(-nodes => [$leaf1,$leaf2] );
                       }

                        print $lca->id; <STDIN>;

                       my $distance2 = $tree->distance( -nodes => [$lca,$leaf2] );

                       print $distance2; <STDIN>;
               }
       }
}

_DATA_
((((((A:1.00000000,B:1.00000000):1.00000000,C:1.00000000):0.00000000,D:0.00000000):1.00000000,(E:0.00000000,(F:2.00000000,G:1.00000000):0.00000000):0.00
000000):2.00000000,(H:3.00000000,(I:2.00000000,(J:1.00000000,(K:2.00000000,(L:2.00000000,M:2.00000000):0.00000000):0.00000000):0.00000000):0.00000000):0
.00000000):1.00000000,(N:0.00000000,((O:0.00000000,P:0.00000000):1.00000000,(Q:2.00000000,(R:2.66666667,S:3.66666667):3.66666667):0.00000000):1.00000000
):3.00000000,(T:0.00000000,(U:0.00000000,V:0.00000000):1.00000000):16.00000000);



 

My ultimate goal is just to conveniently derive the information that nodes M and L share the same LCA O for the following tree.

 

         +---I

         |

     +---M

     |   |

     |   +---H

     |

+---O

|   |

|   |   +---G

|   |   |

|   +---L

|       |

|       +---F

A

|       +---E

|       |

|   +---K

|   |   |

|   |   +---D

|   |

+---N

     |

     |   +---C

     |   |

     +---J

         |

         +---B

 

 

 




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