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
Example 2
phytreeviz -i ./example/small_example.nwk -o cli_example02.png \
--show_branch_length --show_confidence
Example 3
phytreeviz -i ./example/medium_example.nwk -o cli_example03.png \
--fig_height 0.3 --align_leaf_label