Tip-to-tip distance

Distance between two tips in a tree

Command identity

Canonical command:

tip_to_tip_distance

Handler:

tip_to_tip_distance

Aliases:

t2t, t2t_dist

Standalone executables:

pk_tip_to_tip_distance, pk_t2t, pk_t2t_dist

Categories:

Tree summary statistics

Runtime interface

Synopsis

phykit tip_to_tip_distance <tree_zero> [<tip_1>] [<tip_2>] [--all-pairs] [--plot] [--plot-output <plot_output>] [--fig-width <fig_width>] [--fig-height <fig_height>] [--dpi <dpi>] [--no-title] [--title <title>] [--legend-position <legend_position>] [--ylabel-fontsize <ylabel_fontsize>] [--xlabel-fontsize <xlabel_fontsize>] [--title-fontsize <title_fontsize>] [--axis-fontsize <axis_fontsize>] [--colors <colors>] [--ladderize] [--cladogram] [--circular] [--color-file <color_file>] [--json]

Arguments

This table is generated from the live command parser. It is the authoritative source for accepted spellings, required arguments, types, defaults, and choices.

Argument	Required	Type	Default	Choices
tree_zero	true	str	required	any
tip_1	false	str	none	any
tip_2	false	str	none	any
--all-pairs	false	boolean	false	any
--plot	false	boolean	false	any
--plot-output	false	str	tip_to_tip_distance_heatmap.png	any
--fig-width	false	float	none	any
--fig-height	false	float	none	any
--dpi	false	int	300	any
--no-title	false	boolean	false	any
--title	false	str	none	any
--legend-position	false	str	none	any
--ylabel-fontsize	false	float	none	any
--xlabel-fontsize	false	float	none	any
--title-fontsize	false	float	none	any
--axis-fontsize	false	float	none	any
--colors	false	str	none	any
--ladderize	false	boolean	false	any
--cladogram	false	boolean	false	any
--circular	false	boolean	false	any
--color-file	false	str	none	any
--json	false	boolean	false	any

Output and errors

--json provides the command's structured JSON representation. Output-file options: --plot-output. Invalid command syntax exits with status 2. Input validation and scientific limitations are described in the guidance below.

Guidance, interpretation, and examples

Calculate distance between two tips (or leaves) in a phylogeny.

Distances are in substitutions per site.

phykit tip_to_tip_distance <tree_file> <tip_1> <tip_2> [--json]
phykit tip_to_tip_distance <tree_file> --all-pairs [--plot] [--plot-output <path>]
    [--fig-width <float>] [--fig-height <float>] [--dpi <int>] [--no-title] [--title <str>]
    [--legend-position <str>] [--ylabel-fontsize <float>] [--xlabel-fontsize <float>]
    [--title-fontsize <float>] [--axis-fontsize <float>] [--colors <str>] [--ladderize] [--cladogram] [--circular] [--color-file <file>] [--json]

Options:
<tree_file>: first argument after function name should be a tree file
<tip_1>: second argument should be the name of the first tip of interest
<tip_2>: third argument should be the name of the second tip of interest
--all-pairs: optional argument to report all pairwise tip distances
--plot: optional argument to save a clustered distance heatmap (requires --all-pairs)
--plot-output: output path for heatmap (default: tip_to_tip_distance_heatmap.png)
--fig-width: figure width in inches (auto-scaled if omitted)
--fig-height: figure height in inches (auto-scaled if omitted)
--dpi: resolution in DPI (default: 300)
--no-title: hide the plot title
--title: custom title text
--legend-position: legend location (e.g., "upper right", "none" to hide)
--ylabel-fontsize: font size for y-axis labels; 0 to hide
--xlabel-fontsize: font size for x-axis labels; 0 to hide
--title-fontsize: font size for the title
--axis-fontsize: font size for axis labels
--colors: comma-separated colors (hex or named)
--ladderize: ladderize (sort) the tree before plotting
--cladogram: draw cladogram (equal branch lengths, tips aligned) instead of phylogram
--circular: draw circular (radial/fan) phylogram instead of rectangular
--color-file: color annotation file for tip labels, clade ranges, and branch colors (iTOL-inspired TSV format)
--json: optional argument to print results as JSON