necom Documentation

Convert a Newick tree to a complete LaTeX document.

Input:

• A Newick tree file.
• If the file contains multiple trees, only the first tree is processed.
• Use --forest to pass through a file that already contains Forest code.

Notes:

• Styles are stored in the comments of each node.
• Draws a cladogram by default.
• Use --bl to draw a phylogram with branch lengths.
• Underscores (_) in names, labels, comments, and visualization attributes (dot, bar, rec, tri) are replaced with spaces.
• Other LaTeX special characters ({ } \ # $ % & ~ ^) in names, labels, comments, and visualization attributes (dot, bar, rec, tri) are escaped automatically.
• Requires a LaTeX installation with fontspec, xeCJK (for East Asian characters), and the forest package. Compilation can be done with tectonic or latexmk -xelatex.
• Use --no-default-style (--style) / -s to keep the template’s original font setup instead of injecting the default Noto Sans configuration.

Examples:

1. Generate a LaTeX file necom nwk to-tex tree.nwk -o tree.tex

2. Compile with Tectonic tectonic tree.tex

3. Compile with Latexmk latexmk -xelatex tree.tex