Bio::Phylo::IO 0.17 RC6

Bio::Phylo::IO Perl module contains input and output of phylogenetic data.

SYNOPSIS

use Bio::Phylo::IO;

# parsing a tree from a newick string
my $tree_string = (((A,B),C),D);;
my $tree = Bio::Phylo::IO->parse(
-string => $tree_string,

# old parser, always adds node labels
-format => newick,
)->first;

# note: newick parsers return
# Bio::Phylo::Forest! Call
# ->first to retrieve the first
# tree of the forest.

# prints Bio::Phylo::Forest::Tree
print ref $tree, "n";

# parsing a table
my $table_string = qq(A,1,2|B,1,2|C,2,2|D,2,1);
my $matrix = Bio::Phylo::IO->parse(
-string => $table_string,
-format => table,

# Data type, see Bio::Phylo::Parsers::Table
-type => STANDARD,

# field separator
-fieldsep => ,,

# line separator
-linesep => |
);

# prints Bio::Phylo::Matrices::Matrix
print ref $matrix, "n";

# parsing a list of taxa
my $taxa_string = A:B:C:D;
my $taxa = Bio::Phylo::IO->parse(
-string => $taxa_string,
-format => taxlist,
-fieldsep => :
);

# prints Bio::Phylo::Taxa
print ref $taxa, "n";

# matches taxon names in tree to $taxa object
$tree->cross_reference($taxa);

# likewise for matrix
$matrix->cross_reference($taxa);

print Bio::Phylo::IO->unparse(

# pass the tree object,
# crossreferenced to taxa, which
# are crossreferenced to the matrix
-phylo => $tree,
-format => pagel
);

# prints a pagel data file:
#4 2
#A,n1,0.000000,1,2
#B,n1,0.000000,1,2
#n1,n2,0.000000
#C,n2,0.000000,2,2
#n2,n3,0.000000
#D,n3,0.000000,2,1