NEXUS Bioinformatics Support for VS Code

This extension provides robust syntax highlighting and structure validation for NEXUS (.nex, .nxs) files, commonly used in bioinformatics and phylogenetics (PAUP*, MrBayes, BEAST, etc.).

Features

1. Syntax Highlighting

• Matrix Awareness: Nucleotides are only highlighted inside MATRIX blocks.

• Taxon Names: Intelligently identifies taxon names (first word/quoted string on a line) to distinguish them from sequence data.

• Comments: Supports standard NEXUS comments [ ... ].

2. Real-time Validation

The extension automatically checks your file structure and provides error warnings (red squiggles) for:

• NTAX Mismatches: Verifies if NTAX matches the actual number of taxa rows in the matrix.

• NCHAR Mismatches: Verifies if NCHAR matches the longest sequence in the matrix.

• Row Consistency: Warns if a specific taxon row length does not match the defined NCHAR.

Requirements

No external dependencies required.