Template Generation Subcommand Reference (`template create-*`)¶

This page documents all 34 dedicated subcommands under pyitol template (pyitol template create-*). They are functionally equivalent to the unified entry point pyitol template create <type>, but each command accepts only its type-specific parameters — ideal for precise scripting and pipelines, with no need to remember the template_type string.

The unified entry pyitol template create supports 31 types; external-shape-bubble is only available through the dedicated subcommand on this page. Use the unified entry for occasional template generation; use dedicated subcommands for fixed-type batch calls in pipelines.

Common options¶

Unless noted otherwise, the following options apply to every command on this page (defaults taken from source):

Option	Short	Default	Description
`--output`	`-o`	`config_template.txt`	Output template file path
`--taxonomy`	`-t`	(required by most)	Taxonomy table file path
`--tree`	`-r`	(required by most)	Newick tree file path
`--label`	`-l`	varies by type	Dataset label
`--id-column`		`id`	ID column name
`--separator`	`-s`	`TAB`	Data separator: `TAB`/`SPACE`/`COMMA`
`--colors`			Custom color map; JSON (`{"A":"#ff0000"}`) or shorthand (`A:#ff0000,B:#00ff00`)

Unlike the unified entry, dedicated subcommands do not support --force / --no-clobber: if the output file exists, the command errors out. Use a different --output or delete the old file first.

By input dependency, the commands are grouped into three classes: - Datasets: generated from "tree + taxonomy" columns; most require --tree and --taxonomy. - Tree structure: collapse, prune, spacing, coloring, styling, etc. - Advanced: require an external data file (--data / --connections); do not depend on tree or taxonomy.

1. Datasets¶

`pyitol template create-color-strip`¶

Add a classification color strip to terminal branches.

Specific options: --column/-c (required, category column), --colors, --strip-width (default 50), --palette (palette subset name).

pyitol template create-color-strip \
  --taxonomy taxonomy.csv --tree tree.nwk \
  --column Phylum --strip-width 60 --output color_strip.txt

`pyitol template create-branch`¶

Color branches by taxonomy (branch coloring).

Specific options: --column/-c (required), --colors.

pyitol template create-branch \
  --taxonomy taxonomy.csv --tree tree.nwk \
  --column Class --colors '{"A":"#ff0000","B":"#00ff00"}' --output branch.txt

`pyitol template create-simple-bar`¶

Single-value bar chart.

Specific options: --column/-c (required, numeric column), --bar-color (default #3c5484), --bar-width (default 50).

pyitol template create-simple-bar \
  --taxonomy taxonomy.csv --tree tree.nwk \
  --column Abundance --bar-color "#1f77b4" --output simple_bar.txt

`pyitol template create-multi-bar`¶

Multi-value bar chart.

Specific options: --columns/-c (required, comma-separated columns), --colors, --field-labels (comma-separated field labels), --width (default 1000), --alignment (default center).

pyitol template create-multi-bar \
  --taxonomy expr.csv --tree tree.nwk \
  --columns Sample1,Sample2,Sample3 \
  --field-labels S1,S2,S3 --width 1200 --output multi_bar.txt

`pyitol template create-heatmap`¶

Heatmap.

Specific options: --columns/-c (required, comma-separated columns), --gradient (color gradient, comma-separated values, e.g. #ff0000,#ffffff,#0000ff).

pyitol template create-heatmap \
  --taxonomy expr.csv --tree tree.nwk \
  --columns Gene1,Gene2,Gene3 \
  --gradient "#d73027,#ffffbf,#1a9850" --output heatmap.txt

`pyitol template create-symbols`¶

Symbol markers.

Specific options: --column/-c (required), --symbol-type (default diamond; diamond/circle/square/triangle/star), --colors, --size (default 30).

pyitol template create-symbols \
  --taxonomy taxonomy.csv --tree tree.nwk \
  --column Status --symbol-type circle --size 40 --output symbols.txt

`pyitol template create-pie`¶

Pie chart.

Specific options: --columns/-c (required, comma-separated columns), --colors, --pie-size (default 50).

pyitol template create-pie \
  --taxonomy counts.csv --tree tree.nwk \
  --columns CatA,CatB,CatC --pie-size 70 --output pie.txt

`pyitol template create-boxplot`¶

Boxplot; columns point to precomputed min/quartiles/median/max.

Specific options: --min (default column minimum), --q1 (default q1), --median (default median), --q3 (default q3), --max (default maximum), --extremes (extreme-value columns, comma-separated, optional), --color (default #00ff00), --width (default 1500).

pyitol template create-boxplot \
  --taxonomy stats.csv --tree tree.nwk \
  --min minimum --q1 q1 --median median --q3 q3 --max maximum \
  --color "#4c78a8" --output boxplot.txt

`pyitol template create-gradient`¶

Numeric gradient color strip.

Specific options: --column/-c (required), --color-min (default #ff0000), --color-max (default #0000ff), --strip-width (default 25), --use-mid-color (flag, enable mid color), --color-mid (default #ffff00).

pyitol template create-gradient \
  --taxonomy taxonomy.csv --tree tree.nwk \
  --column Value --color-min "#ff0000" --color-max "#0000ff" \
  --use-mid-color --color-mid "#ffff00" --output gradient.txt

`pyitol template create-labels`¶

Rename / customize terminal labels.

Specific options: --column/-c (required, label column).

pyitol template create-labels \
  --taxonomy taxonomy.csv --tree tree.nwk \
  --column DisplayName --output labels.txt

`pyitol template create-popup-info`¶

Popup info shown on hover (title + content).

Specific options: --title-column (default title), --content-column (default content).

pyitol template create-popup-info \
  --taxonomy taxonomy.csv --tree tree.nwk \
  --title-column Species --content-column Description --output popup.txt

`pyitol template create-binary`¶

Binary dataset; converts category columns to 0/1 fields.

Specific options: --columns/-c (required, comma-separated category columns), --field-colors (default #ff0000,#00ff00,#0000ff), --field-shapes (default 1,2,3, values 1–6), --color (default #ff0000), --show-internal (default 1).

pyitol template create-binary \
  --taxonomy taxonomy.csv --tree tree.nwk \
  --columns Trait1,Trait2,Trait3 \
  --field-colors "#e41a1c,#377eb8,#4daf4a" --output binary.txt

`pyitol template create-text`¶

Text labels next to each node.

Specific options: --column/-c (required), --font-size (default 12), --font-style (default normal).

pyitol template create-text \
  --taxonomy taxonomy.csv --tree tree.nwk \
  --column Note --font-size 14 --output text.txt

`pyitol template create-external-shape`¶

External shape markers drawn outside the tree.

Specific options: --column/-c (required), --shape-type (default circle; circle/square/star/triangle_right/triangle_left/checkmark), --colors, --size (default 20).

pyitol template create-external-shape \
  --taxonomy taxonomy.csv --tree tree.nwk \
  --column Group --shape-type star --size 25 --output ext_shape.txt

`pyitol template create-connections`¶

Connection lines. Does not depend on tree or taxonomy; reads a connections JSON file.

Specific options: --connections/-c (required, JSON file path, format [[id1,id2],...]), --color (default #e64b35), --line-width (default 2), --line-type (default solid; solid/dotted/dashed), --arrow-head-size (default 1).

# pairs.json: [["TaxonA","TaxonB"], ["TaxonC","TaxonD"]]
pyitol template create-connections \
  --connections pairs.json --color "#e64b35" --line-type dashed --output connections.txt

`pyitol template create-domains`¶

Protein domains. Does not depend on tree or taxonomy; reads a JSON data file.

Specific options: --data/-d (required, JSON file path), --color (default #ff00aa), --scale (optional).

# domains.json: [{"id":"TaxonA","domains":[{"start":1,"end":50,"name":"PF001","color":"#ff0000"}]}]
pyitol template create-domains \
  --data domains.json --color "#ff00aa" --output domains.txt

2. Tree Structure¶

`pyitol template create-tree-colors`¶

Tree colors; supports branch, label, branch-width, range, and gradient coloring.

Specific options: --column/-c (required), --colors, --color-type (default clade; clade/label/branch/width/range/gradient), --width-value (default 3, only for width type).

# Color by branch
pyitol template create-tree-colors \
  --taxonomy taxonomy.csv --tree tree.nwk \
  --column Phylum --color-type branch --output tree_colors_branch.txt

# Color by numeric gradient
pyitol template create-tree-colors \
  --taxonomy taxonomy.csv --tree tree.nwk \
  --column Score --color-type gradient --output tree_colors_grad.txt

`pyitol template create-branch-gradient`¶

Branch gradient based on a numeric column.

Specific options: --column/-c (required), --color-min (default #ff0000), --color-max (default #0000ff), --use-mid-color (flag), --color-mid (default #ffff00).

pyitol template create-branch-gradient \
  --taxonomy taxonomy.csv --tree tree.nwk \
  --column Distance --color-min "#fee090" --color-max "#4575b4" --output branch_grad.txt

`pyitol template create-collapse`¶

Collapse clades. Two modes: 1. --node-ids directly specifies node IDs; 2. --taxon + --rank + --taxonomy + --tree finds a taxon by name (checks monophyly first).

Non-monophyletic groups are skipped by default; --strict aborts instead.

Specific options: --node-ids/-n (comma-separated), --taxon, --rank, --taxonomy/-t, --tree/-r, --strict (flag).

# Mode 1: by node IDs
pyitol template create-collapse \
  --node-ids "TaxonA,TaxonB" --output collapse_ids.txt

# Mode 2: by taxon name (checks monophyly first)
pyitol template create-collapse \
  --taxonomy taxonomy.csv --tree tree.nwk \
  --taxon Cyanobacteriota --rank Phylum --strict --output collapse_taxon.txt

`pyitol template create-prune`¶

Prune branches (remove specified nodes). Does not depend on tree or taxonomy.

Specific options: --node-ids/-n (required, comma-separated).

pyitol template create-prune \
  --node-ids "TaxonX,TaxonY,TaxonZ" --output prune.txt

`pyitol template create-spacing`¶

Node spacing. Does not depend on tree or taxonomy; reads a CSV with id and factor columns.

Specific options: --data/-d (required, CSV file path).

# spacing.csv: id,factor
# TaxonA,2.0
# TaxonB,0.5
pyitol template create-spacing --data spacing.csv --output spacing.txt

`pyitol template create-ranges`¶

Colored ranges; draws continuous background ranges grouped by a column.

Specific options: --column/-c (required), --colors.

pyitol template create-ranges \
  --taxonomy taxonomy.csv --tree tree.nwk \
  --column Biome --colors '{"Marine":"#1f77b4","Soil":"#aec7e8"}' --output ranges.txt

`pyitol template create-highlight`¶

Label background highlight.

Specific options: --column/-c (required), --colors.

pyitol template create-highlight \
  --taxonomy taxonomy.csv --tree tree.nwk \
  --column Category --colors '{"Pathogenic":"#d62728"}' --output highlight.txt

`pyitol template create-style`¶

Branch / label style (line style, font, background).

Specific options: --column/-c (required), --style-type (default branch; branch/label/label_background), --colors, --line-style (default normal; normal/dashed/dotted), --font (default Arial), --size (default 1).

pyitol template create-style \
  --taxonomy taxonomy.csv --tree tree.nwk \
  --column Lineage --style-type branch --line-style dashed --output style.txt

`pyitol template create-arrow`¶

Arrow annotations. Does not depend on tree or taxonomy; reads a CSV with id, position, direction, color columns.

Specific options: --data-file/-d (required, CSV file path), --color (default #ff0000), --arrow-size (default 30).

# arrows.csv: id,position,direction,color
# TaxonA,0.5,right,#ff0000
pyitol template create-arrow --data-file arrows.csv --arrow-size 40 --output arrows.txt

3. Advanced¶

`pyitol template create-linechart`¶

Line chart drawn beside the tree.

Specific options: --column/-c (required, numeric column), --position-column/-p (position column, defaults to row index), --color (default #3c5484), --line-width (default 2).

pyitol template create-linechart \
  --taxonomy expr.csv --tree tree.nwk \
  --column Expression --position-column Time --output linechart.txt

`pyitol template create-image`¶

Embed images beside nodes (file or URL).

Specific options: --image-column/-i (required, image filename column), --url-column/-u (image URL column, optional), --image-width (default 50).

pyitol template create-image \
  --taxonomy taxonomy.csv --tree tree.nwk \
  --image-column PhotoFile --url-column PhotoURL --image-width 60 --output images.txt

`pyitol template create-alignment`¶

Sequence alignment display.

Specific options: --alignment-column/-a (required, alignment column), --color-scheme (default nucleotide; nucleotide/amino_acid).

pyitol template create-alignment \
  --taxonomy taxonomy.csv --tree tree.nwk \
  --alignment-column AlignedSeq --color-scheme amino_acid --output alignment.txt

`pyitol template create-tanglegram`¶

Tanglegram connecting corresponding nodes between two trees. Does not depend on tree or taxonomy.

Specific options: --connections/-c (required, format id1,id2;id3,id4), --color (default #999999), --line-width (default 1).

pyitol template create-tanglegram \
  --connections "TaxonA,TaxonA2;TaxonB,TaxonB2" \
  --color "#999999" --output tanglegram.txt

`pyitol template create-placement`¶

Phylogenetic placement. Does not depend on tree or taxonomy; reads a CSV with id, position, count, color columns.

Specific options: --data-file/-d (required, CSV file path), --color (default #ff0000), --spacing (default 5).

# placement.csv: id,position,count,color
# Query1,0.8,12,#ff0000
pyitol template create-placement --data-file placement.csv --spacing 8 --output placement.txt

`pyitol template create-timescale`¶

Timescale ticks on branches. Does not depend on tree or taxonomy; reads a CSV with time_point, label, color columns.

Specific options: --data-file/-d (required, CSV file path), --color (default #000000), --scale-position (default bottom; top/bottom/both).

# timescale.csv: time_point,label,color
# 0.5,Middle,#000000
pyitol template create-timescale --data-file timescale.csv --scale-position both --output timescale.txt

`pyitol template create-meme`¶

MEME motifs. Does not depend on tree or taxonomy; reads a CSV with id, start, end, name, color columns.

Specific options: --data-file/-d (required, CSV file path), --color (default #ff0000), --show-labels (default 1).

# meme.csv: id,start,end,name,color
# Seq1,10,30,Motif1,#ff0000
pyitol template create-meme --data-file meme.csv --show-labels 1 --output meme.txt

`pyitol template create-manual`¶

Manual annotation with free-form custom data. Does not depend on tree or taxonomy; reads an arbitrary-column CSV.

Specific options: --data-file/-d (required, CSV file path), --color (default #ff0000), --custom-header (custom header JSON, e.g. {"KEY":"VALUE"}).

pyitol template create-manual \
  --data-file custom.csv --custom-header '{"FIELD_SHAPE":"1"}' --output manual.txt

`pyitol template create-external-shape-bubble`¶

Multi-column bubble external shapes.

Specific options: --columns/-c (required, comma-separated numeric columns).

pyitol template create-external-shape-bubble \
  --taxonomy expr.csv --tree tree.nwk \
  --columns Metric1,Metric2,Metric3 --output bubble.txt

CLI Reference: command overview, the unified template create entry, global options, and exit codes.
Template Tutorial: selecting and combining 30+ template types.
API Guide: iTOL batch API and Python API usage.

Template Generation Subcommand Reference (template create-*)¶

Common options¶

1. Datasets¶

pyitol template create-color-strip¶

pyitol template create-branch¶

pyitol template create-simple-bar¶

pyitol template create-multi-bar¶

pyitol template create-heatmap¶

pyitol template create-symbols¶

pyitol template create-pie¶

pyitol template create-boxplot¶

pyitol template create-gradient¶

pyitol template create-labels¶

pyitol template create-popup-info¶

pyitol template create-binary¶

pyitol template create-text¶

pyitol template create-external-shape¶

pyitol template create-connections¶

pyitol template create-domains¶

2. Tree Structure¶

pyitol template create-tree-colors¶

pyitol template create-branch-gradient¶

pyitol template create-collapse¶

pyitol template create-prune¶

pyitol template create-spacing¶

pyitol template create-ranges¶

pyitol template create-highlight¶

pyitol template create-style¶

pyitol template create-arrow¶

3. Advanced¶

pyitol template create-linechart¶

pyitol template create-image¶

pyitol template create-alignment¶

pyitol template create-tanglegram¶

pyitol template create-placement¶

pyitol template create-timescale¶

pyitol template create-meme¶

pyitol template create-manual¶

pyitol template create-external-shape-bubble¶

Related pages¶

Template Generation Subcommand Reference (`template create-*`)¶

`pyitol template create-color-strip`¶

`pyitol template create-branch`¶

`pyitol template create-simple-bar`¶

`pyitol template create-multi-bar`¶

`pyitol template create-heatmap`¶

`pyitol template create-symbols`¶

`pyitol template create-pie`¶

`pyitol template create-boxplot`¶

`pyitol template create-gradient`¶

`pyitol template create-labels`¶

`pyitol template create-popup-info`¶

`pyitol template create-binary`¶

`pyitol template create-text`¶

`pyitol template create-external-shape`¶

`pyitol template create-connections`¶

`pyitol template create-domains`¶

`pyitol template create-tree-colors`¶

`pyitol template create-branch-gradient`¶

`pyitol template create-collapse`¶

`pyitol template create-prune`¶

`pyitol template create-spacing`¶

`pyitol template create-ranges`¶

`pyitol template create-highlight`¶

`pyitol template create-style`¶

`pyitol template create-arrow`¶

`pyitol template create-linechart`¶

`pyitol template create-image`¶

`pyitol template create-alignment`¶

`pyitol template create-tanglegram`¶

`pyitol template create-placement`¶

`pyitol template create-timescale`¶

`pyitol template create-meme`¶

`pyitol template create-manual`¶

`pyitol template create-external-shape-bubble`¶