Newick and NEXUS File Formats Explained

When working with phylogenetic trees, you'll encounter two dominant file formats: Newick and NEXUS. Understanding these formats is essential for data exchange between different phylogenetic software.

Newick Format

The Newick format (also called New Hampshire format) is a simple, compact way to represent tree topology using nested parentheses.

Basic Syntax

• Parentheses () define clades
• Commas , separate taxa or clades
• Colons : precede branch lengths
• Semicolon ; terminates the tree

Examples

# Simple tree with 3 taxa
(A,B,C);

# Tree with topology: A is sister to (B,C)
(A,(B,C));

# Tree with branch lengths
(A:0.1,B:0.2,(C:0.3,D:0.4):0.5);

# Tree with internal node labels (support values)
(A:0.1,B:0.2,(C:0.3,D:0.4)90:0.5);

# Rooted tree with branch lengths
((A:0.1,B:0.2):0.3,(C:0.3,D:0.4):0.5);

Reading Newick Trees

To read a Newick string, start from the innermost parentheses and work outward:

((A,B),(C,D));

Read as:
- A and B form a clade
- C and D form a clade
- These two clades are sisters

NEXUS Format

NEXUS is a more comprehensive format that can store trees, character matrices, and analysis settings in a single file.

Basic Structure

#NEXUS

BEGIN TAXA;
    DIMENSIONS NTAX=4;
    TAXLABELS
        Taxon_A
        Taxon_B
        Taxon_C
        Taxon_D
    ;
END;

BEGIN TREES;
    TREE tree1 = ((Taxon_A,Taxon_B),(Taxon_C,Taxon_D));
END;

NEXUS Blocks

NEXUS files contain different blocks for different data types:

• TAXA: List of taxon names
• CHARACTERS/DATA: Character matrix (DNA, morphology)
• TREES: One or more phylogenetic trees
• ASSUMPTIONS: Character weights, type sets
• SETS: Taxon sets, character sets
• PAUP/MRBAYES: Software-specific commands

Character Matrix Example

#NEXUS

BEGIN DATA;
    DIMENSIONS NTAX=4 NCHAR=10;
    FORMAT DATATYPE=DNA GAP=- MISSING=?;
    MATRIX
        Taxon_A  ATGCATGCAT
        Taxon_B  ATGCATGCAT
        Taxon_C  ATGGATGCAT
        Taxon_D  ATGGATGCGT
    ;
END;

BEGIN TREES;
    TREE best = ((Taxon_A,Taxon_B),(Taxon_C,Taxon_D));
END;

Comparison

Special Characters

Some characters require special handling in both formats:

• Spaces: Use underscores or quote taxon names
• Parentheses, commas, colons: Quote names containing these
• Apostrophes: Use double apostrophes inside quoted names

# Taxon names with spaces
('Homo sapiens','Pan troglodytes');

# Using underscores instead
(Homo_sapiens,Pan_troglodytes);

Converting Between Formats

Many tools can convert between Newick and NEXUS:

• PhyloVerse: Import either format, export both
• FigTree: Open and save in multiple formats
• R (ape package): read.tree(), read.nexus(), write.tree()
• Biopython: Phylo module handles both formats