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phyTreeViz CLI Document

Usage

Basic Command

phytreeviz -i [Tree file or text] -o [Tree visualization file]

Options

General Options:
  -i IN, --intree IN      Input phylogenetic tree file or text
  -o OUT, --outfile OUT   Output phylogenetic tree plot file [*.png|*.jpg|*.svg|*.pdf]
  --format                Input phylogenetic tree format (Default: 'newick')
  -v, --version           Print version information
  -h, --help              Show this help message and exit

Figure Appearence Options:
  --fig_height            Figure height per leaf node of tree (Default: 0.5)
  --fig_width             Figure width (Default: 8.0)
  --leaf_label_size       Leaf label size (Default: 12)
  --ignore_branch_length  Ignore branch length for plotting tree (Default: OFF)
  --align_leaf_label      Align leaf label position (Default: OFF)
  --show_branch_length    Show branch length (Default: OFF)
  --show_confidence       Show confidence (Default: OFF)
  --dpi                   Figure DPI (Default: 300)

Available Tree Format: ['newick', 'phyloxml', 'nexus', 'nexml', 'cdao']

Example Command

Click here to download example tree files.

Example 1

phytreeviz -i "((A,B),((C,D),(E,(F,G))));" -o cli_example01.png

example01.png

Example 2

phytreeviz -i ./example/small_example.nwk -o cli_example02.png \
           --show_branch_length --show_confidence

example02.png

Example 3

phytreeviz -i ./example/medium_example.nwk -o cli_example03.png \
           --fig_height 0.3 --align_leaf_label

example03.png