---
name: "Bio::TreeIO"
section: "3pm"
platform: "linux"
package: "libbio-perl-perl"
version: "1.7.8-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::TreeIO"
---

# Bio::TreeIO(3pm)

Parser for Tree files

## NAME

Bio::TreeIO - Parser for Tree files

## SYNOPSIS

```
  {
      use Bio::TreeIO;
      my $treeio = Bio::TreeIO->new(-format => 'newick',
                                    -file   => 'globin.dnd');
      while( my $tree = $treeio->next_tree ) {
                print "Tree is ", $tree->number_nodes, "\n";
      }
  }
```

## DESCRIPTION

This is the driver module for Tree reading from data streams and flatfiles.  This is intended to be able to create Bio::Tree::TreeI objects.

## FEEDBACK

### Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list.  Your participation is much appreciated.

```
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
```

### Support

Please direct usage questions or support issues to the mailing list:

*bioperl-l@bioperl.org*

rather than to the module maintainer directly. Many experienced and  reponsive experts will be able look at the problem and quickly  address it. Please include a thorough description of the problem  with code and data examples if at all possible.

### 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 the web:

```
  https://github.com/bioperl/bioperl-live/issues
```

## AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

## CONTRIBUTORS

Allen Day \<allenday@ucla.edu\>

## 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 = Bio::TreeIO->new();
 Function: Builds a new Bio::TreeIO object
 Returns : Bio::TreeIO
 Args    : a hash.  useful keys:
   -format : Specify the format of the file.  Supported formats:
     newick             Newick tree format
     nexus              Nexus tree format
     nhx                NHX tree format
     svggraph           SVG graphical representation of tree
     tabtree            ASCII text representation of tree
     lintree            lintree output format
```

### format

```
 Title   : format
 Usage   : $format = $obj->format()
 Function: Get the tree format
 Returns : tree format
 Args    : none
```

### next\_tree

```
 Title   : next_tree
 Usage   : my $tree = $treeio->next_tree;
 Function: Gets the next tree off the stream
 Returns : Bio::Tree::TreeI or undef if no more trees
 Args    : none
```

### write\_tree

```
 Title   : write_tree
 Usage   : $treeio->write_tree($tree);
 Function: Writes a tree onto the stream
 Returns : none
 Args    : Bio::Tree::TreeI
```

### attach\_EventHandler

```
 Title   : attach_EventHandler
 Usage   : $parser->attatch_EventHandler($handler)
 Function: Adds an event handler to listen for events
 Returns : none
 Args    : Bio::Event::EventHandlerI
```

### \_eventHandler

```
 Title   : _eventHandler
 Usage   : private
 Function: Get the EventHandler
 Returns : Bio::Event::EventHandlerI
 Args    : none
```

### \_load\_format\_module

```
 Title   : _load_format_module
 Usage   : *INTERNAL TreeIO stuff*
 Function: Loads up (like use) a module at run time on demand
 Example :
 Returns :
 Args    :
```

### \_guess\_format

```
 Title   : _guess_format
 Usage   : $obj->_guess_format($filename)
 Function:
 Example :
 Returns : guessed format of filename (lower case)
 Args    :
```