External Format Support

class Phyloxml:
    """
    PhyloXML format parser and writer for phylogenetic data exchange.
    """
    
    def __init__(self):
        """Initialize PhyloXML handler."""

    def build_from_file(self, fname):
        """
        Parse PhyloXML file and build tree structure.

        Parameters:
        - fname (str): Path to PhyloXML file

        Returns:
        PhyloxmlTree: Parsed phylogenetic tree with PhyloXML annotations
        """

    def export(self, outfile=None):
        """
        Export tree to PhyloXML format.

        Parameters:
        - outfile (str): Output file path, if None returns string

        Returns:
        str: PhyloXML formatted string (if outfile is None)
        """

class PhyloxmlTree(PhyloTree):
    """
    Phylogenetic tree with PhyloXML-specific features and annotations.
    """
    
    def __init__(self, phyloxml_file=None):
        """
        Initialize PhyloXML tree.

        Parameters:
        - phyloxml_file (str): Path to PhyloXML file to load
        """

    # PhyloXML-specific properties
    phyloxml: dict          # PhyloXML annotations and metadata
    confidence: float       # Confidence value for branches
    taxonomy: dict          # Taxonomic information
    sequence: dict          # Sequence data and annotations
    events: dict           # Evolutionary events (duplication, speciation)
    properties: dict       # Custom properties from PhyloXML

class Nexml:
    """
    NeXML format parser and writer for phylogenetic data exchange.
    """
    
    def __init__(self):
        """Initialize NeXML handler."""

    def build_from_file(self, fname):
        """
        Parse NeXML file and build tree structure.

        Parameters:
        - fname (str): Path to NeXML file

        Returns:
        NexmlTree: Parsed phylogenetic tree with NeXML annotations
        """

    def export(self, outfile=None):
        """
        Export tree to NeXML format.

        Parameters:
        - outfile (str): Output file path, if None returns string

        Returns:
        str: NeXML formatted string (if outfile is None)
        """

class NexmlTree(PhyloTree):
    """
    Phylogenetic tree with NeXML-specific features and annotations.
    """
    
    def __init__(self, nexml_file=None):
        """
        Initialize NeXML tree.

        Parameters:
        - nexml_file (str): Path to NeXML file to load
        """

    # NeXML-specific properties
    nexml: dict            # NeXML annotations and metadata
    otus: dict            # Operational Taxonomic Units information
    characters: dict       # Character data and matrices
    meta: dict            # Metadata annotations

def read_newick(newick_string, root_node=None, format=0, quoted_node_names=False):
    """
    Parse Newick format string with extensive format support.

    Parameters:
    - newick_string (str): Newick formatted tree string
    - root_node (TreeNode): Existing node to use as root
    - format (int): Newick subformat (0-9)
        0: flexible with support values  
        1: flexible with internal node names
        2: all branches + leaf names + internal supports
        3: all branches + all names  
        4: leaf branches + leaf names
        5: internal and leaf branches + leaf names
        6: internal branches + leaf names
        7: leaf branches + all names
        8: all names
        9: leaf names
    - quoted_node_names (bool): Handle quoted node names with special characters

    Returns:
    TreeNode: Parsed tree structure
    """

def write_newick(tree, features=None, format=0, format_root_node=True, 
                is_leaf_fn=None, quoted_node_names=False):
    """
    Export tree to Newick format with customizable options.

    Parameters:
    - tree (TreeNode): Tree to export
    - features (list): Node features to include in output
    - format (int): Newick output format (0-9)
    - format_root_node (bool): Include root node in output
    - is_leaf_fn (function): Custom function to determine leaf nodes
    - quoted_node_names (bool): Quote node names with special characters

    Returns:
    str: Newick formatted string
    """

# FASTA format with phylogenetic extensions
def read_fasta_with_tree(fasta_file, tree_file=None):
    """
    Read FASTA sequences and optionally associate with tree.

    Parameters:
    - fasta_file (str): Path to FASTA file
    - tree_file (str): Optional tree file for sequence-tree association

    Returns:
    tuple: (SeqGroup, PhyloTree) if tree_file provided, else SeqGroup
    """

# PHYLIP format variations
def read_phylip(source, interleaved=False, relaxed=False, tree_names=True):
    """
    Read PHYLIP format with tree compatibility options.

    Parameters:
    - source (str): PHYLIP file path or string
    - interleaved (bool): Interleaved PHYLIP format
    - relaxed (bool): Relaxed naming (>10 characters)
    - tree_names (bool): Ensure names compatible with tree formats

    Returns:
    SeqGroup: Parsed sequences
    """

# Nexus format support  
def read_nexus(nexus_file):
    """
    Read Nexus format files containing trees and/or data.

    Parameters:
    - nexus_file (str): Path to Nexus file

    Returns:
    dict: Dictionary containing trees, data, and metadata
    """

def detect_format(filename):
    """
    Automatically detect file format based on content and extension.

    Parameters:
    - filename (str): Path to file

    Returns:
    str: Detected format ("newick", "phyloxml", "nexml", "nexus", "fasta", "phylip")
    """

def auto_parse(filename, **kwargs):
    """
    Automatically parse file using detected format.

    Parameters:
    - filename (str): File to parse
    - kwargs: Format-specific parsing options

    Returns:
    Tree or SeqGroup: Parsed data structure
    """

class WebTreeApplication:
    """
    Web-based tree visualization application for interactive tree exploration.
    """
    
    def __init__(self, tree, name=None, host="localhost", port=8080):
        """
        Initialize web tree application.

        Parameters:
        - tree (Tree): Tree to visualize
        - name (str): Application name
        - host (str): Server host address
        - port (int): Server port number
        """

    def launch(self, open_browser=True):
        """
        Launch web server for tree visualization.

        Parameters:
        - open_browser (bool): Automatically open browser

        Returns:
        str: URL of launched application
        """

    def add_tree(self, tree, name=None):
        """
        Add additional tree to web application.

        Parameters:
        - tree (Tree): Tree to add
        - name (str): Tree identifier
        """

    def set_tree_style(self, tree_style):
        """
        Set default tree style for web display.

        Parameters:
        - tree_style (TreeStyle): Style configuration
        """

class PhylomeDB3Connector:
    """
    Interface to PhylomeDB3 phylogenomic database.
    """
    
    def __init__(self, host="phylomedb.org"):
        """
        Initialize PhylomeDB connector.

        Parameters:
        - host (str): PhylomeDB server hostname
        """

    def get_best_tree(self, seed_taxid, target_taxid=None):
        """
        Retrieve best phylogenetic tree for given taxonomic IDs.

        Parameters:
        - seed_taxid (int): Seed species taxonomic ID
        - target_taxid (int): Target species taxonomic ID (optional)

        Returns:
        PhyloTree: Best available phylogenetic tree
        """

    def search_trees(self, seed_taxid, target_species=None):
        """
        Search for trees containing specified taxa.

        Parameters:
        - seed_taxid (int): Seed taxonomic ID
        - target_species (list): Target species list

        Returns:
        list: Available trees matching criteria
        """

    def get_tree_ages(self, phylome_id):
        """
        Get age estimates for trees in phylome.

        Parameters:
        - phylome_id (int): PhylomeDB phylome identifier

        Returns:
        dict: Age estimates for phylome trees
        """

from ete3 import Phyloxml, PhyloxmlTree

# Parse PhyloXML file
phyloxml_parser = Phyloxml()
tree = phyloxml_parser.build_from_file("example.phyloxml")

# Access PhyloXML-specific data
for node in tree.traverse():
    if hasattr(node, 'confidence'):
        print(f"Node confidence: {node.confidence}")
    if hasattr(node, 'taxonomy'):
        print(f"Taxonomy: {node.taxonomy}")

# Export with annotations
output_xml = phyloxml_parser.export("output.phyloxml")

from ete3 import Nexml, NexmlTree

# Parse NeXML file
nexml_parser = Nexml()
tree = nexml_parser.build_from_file("data.nexml")

# Access NeXML metadata
if hasattr(tree, 'meta'):
    print(f"Metadata: {tree.meta}")

# Work with character data
if hasattr(tree, 'characters'):
    print(f"Character matrix: {tree.characters}")

# Export to NeXML
nexml_parser.export("output.nexml")

from ete3 import Tree, Phyloxml, Nexml

# Load tree in Newick format
tree = Tree("(A:1,(B:1,C:1):0.5);")

# Convert to PhyloXML
phyloxml = Phyloxml()
tree.phyloxml = {"description": "Example tree"}
phyloxml_output = phyloxml.export()

# Convert to NeXML
nexml = Nexml()
tree.nexml = {"title": "Example phylogeny"}
nexml_output = nexml.export()

# Save in different formats
with open("tree.phyloxml", "w") as f:
    f.write(phyloxml_output)
    
with open("tree.nexml", "w") as f:
    f.write(nexml_output)

from ete3 import detect_format, auto_parse

# Detect format automatically
file_format = detect_format("unknown_format_file.txt")
print(f"Detected format: {file_format}")

# Parse automatically based on format
data = auto_parse("phylogenetic_data.xml")

if isinstance(data, Tree):
    print(f"Parsed tree with {len(data)} nodes")
elif isinstance(data, SeqGroup):
    print(f"Parsed {len(data)} sequences")

from ete3 import Tree, WebTreeApplication, TreeStyle

# Create tree and style
tree = Tree("(human:1,(chimp:0.5,bonobo:0.5):0.5);")
ts = TreeStyle()
ts.show_leaf_name = True
ts.show_branch_length = True

# Launch web application
webapp = WebTreeApplication(tree, name="Primate Tree")
webapp.set_tree_style(ts)
url = webapp.launch()

print(f"Tree visualization available at: {url}")

from ete3 import PhylomeDB3Connector

# Connect to PhylomeDB
phylomedb = PhylomeDB3Connector()

# Search for trees
human_trees = phylomedb.search_trees(seed_taxid=9606)  # Human
print(f"Found {len(human_trees)} trees with human sequences")

# Get best tree
best_tree = phylomedb.get_best_tree(seed_taxid=9606, target_taxid=9598)  # Human-chimp
print(f"Best tree: {best_tree.get_ascii()}")

# Get age estimates
ages = phylomedb.get_tree_ages(phylome_id=1)
print(f"Age estimates: {ages}")

from ete3 import Tree, SeqGroup, Phyloxml, NCBITaxa

# Multi-format phylogenetic workflow
def process_phylogenetic_data(tree_file, sequence_file=None):
    # Auto-detect and parse tree
    tree_format = detect_format(tree_file)
    tree = auto_parse(tree_file)
    
    # Load sequences if provided
    if sequence_file:
        seq_format = detect_format(sequence_file)
        sequences = auto_parse(sequence_file)
        
        # Link sequences to tree
        if isinstance(tree, PhyloTree):
            tree.link_to_alignment(sequences)
    
    # Add taxonomic information
    ncbi = NCBITaxa()
    tree = ncbi.annotate_tree(tree)
    
    # Export in multiple formats
    results = {
        'newick': tree.write(format=1),
        'phyloxml': None,
        'ascii': tree.get_ascii()
    }
    
    # Export to PhyloXML with annotations
    if hasattr(tree, 'taxonomy'):
        phyloxml = Phyloxml()
        results['phyloxml'] = phyloxml.export()
    
    return tree, results

# Process data
tree, outputs = process_phylogenetic_data("input.nw", "sequences.fasta")

# Save all formats
for format_name, content in outputs.items():
    if content:
        with open(f"output.{format_name}", "w") as f:
            f.write(content)