necom Documentation

Reformat a Newick tree to make its structure easier to read.

Input:

• A Newick tree file.

Notes:

• By default, prints the tree indented with two spaces (--text / -t “ “).
• Use --text / -t to customize the indentation string.
• Use --compact / -c to output the tree as a single line.
• The default output is valid Newick.
• Using non-whitespace characters for --text may produce invalid Newick.

Examples:

1. Default indentation necom nwk indent tree.nwk

2. Compact output necom nwk indent tree.nwk --compact

3. Indent with visual guides (not valid Newick) necom nwk indent tree.nwk --text ". "