LaTeX Forest Output

necom nwk to-forest and necom nwk to-tex convert Newick trees into LaTeX code using the Forest package. This is useful for producing publication-quality phylogenetic trees directly from the command line.

• to-forest emits raw Forest code that can be embedded into an existing LaTeX document.
• to-tex generates a complete .tex document by merging the Forest code with a built-in template, ready for compilation with xelatex or tectonic.

Core Commands

necom nwk to-forest

Generates raw LaTeX Forest code.

necom nwk to-forest tree.nwk

Use --bl to draw a phylogram with branch lengths instead of a cladogram:

necom nwk to-forest tree.nwk --bl

necom nwk to-tex

Generates a complete LaTeX document.

necom nwk to-tex tree.nwk -o tree.tex

Compile the output:

tectonic tree.tex
# or
latexmk -xelatex tree.tex

Use --forest to pass through an existing Forest code file instead of a Newick tree:

necom nwk to-tex forest.tex --forest -o document.tex

Style System

Styles are attached to nodes as NHX annotations. The template defines four core visual attributes:

dot

Draws a filled circle at the node.

[&&NHX:dot=red]

When no color is given, dot is automatically applied to named internal nodes.

bar

Draws a short perpendicular bar on the edge between the node and its parent. Useful for marking events or character-state changes.

[&&NHX:bar=blue]

rec

Draws a background rectangle behind the entire clade rooted at the node.

[&&NHX:rec=LemonChiffon]

This is often combined with the soft palette defined in the template.

tri

Draws a triangle to the right of the node, commonly used for collapsed clades or to emphasize a leaf.

[&&NHX:tri=green]

Colors and Global Settings

The built-in template provides a soft, muted palette (for example ChampagnePink, TeaRose, and Celadon). By default:

• tier=word is enabled, aligning all leaf nodes at the same level (cladogram style).
• Branch lines are gray (1 pt).
• Nodes are drawn as small black circles (2 pt).
• A sans-serif font is used.

Font behavior:

• By default, the template uses Noto Sans, which is widely available.
• Use --no-default-style to keep the template’s original Fira Sans / Source Han Sans SC setup instead of injecting the default Noto Sans configuration.

Advanced Features

Phylogram Mode (--bl)

When the input tree contains branch lengths, --bl produces a phylogram with a automatically computed scale bar. The scale values (e.g., 0.01, 0.05, 1.0) are chosen based on the tree height and rendered in the lower-right corner.

Forest Pass-Through (--forest)

to-tex --forest allows an externally generated Forest code file to be wrapped in the template. This is useful when the Forest code has been produced by to-forest and then manually adjusted.

Special Character Handling

LaTeX special characters and Newick conventions are normalized automatically:

• Underscores (_) in node names are replaced with spaces.
• LaTeX special characters ({ } \ # $ % & ~ ^) in node names, labels, comments, and visualization attributes are escaped.

This ensures that the generated Forest code compiles without manual cleanup.

Workflow Example

1. Annotate the tree with visualization attributes:

necom nwk comment input.nwk --lca A,B --rec TeaRose --label Group1 > annotated.nwk

2. Generate the LaTeX document:

necom nwk to-tex annotated.nwk -o output.tex

3. Compile:

tectonic output.tex

Requirements

Compiling to-tex output requires a LaTeX installation that includes:

• fontspec
• xeCJK (for East Asian characters)
• forest

Tectonic is the recommended compiler, but latexmk -xelatex also works.