This script can be used to draw nice looking phylogenetic trees. It's combined with a csv file of annotations for the leaves and a configureation file that can set up the tree for common opperations such as collapsing and highlighting clades.

This script is built on ete3 which must be installed and working correctly and additionally requires pyYAML for parsing the configuration file.

The annotation file is a comma separated values (csv) file where each row contains information about each leaf in the tree. The file must contain a header row! The column headers must be simply named, no spaces, no special characters are allowed in the column headers. One of the columns must be the name of the leaf in the tree file

The configuration file is a YAML formatted file that is used to specify grouping and highlighting of leaves in the tree. The following options are available

The outgroup for the tree can be specified by one of three ways. First, a single leaf name can be used; Second, a list of leaf names can be given, in which case the lowest common ancestor of the leaves will be used as the node in the tree to root on; third, the word 'midpoint' can be used to specify that the tree should be rooted at the midpoint node of the tree.

outgroup: 'leaf name'
outgroup: ['leaf name 1', 'leaf name 2', 'leaf name 3']
outgroup: 'midpoint'

The leaf IDs in the tree file have to match up with one one the columns of the annotation file. In the configuration file give the name of the column in the annotations file that corresponds to the leaf name using the leaf_name_column

leaf_name_column: Id

Provide the format for the leaf labels on the tree using python's format style. The names of the arguments are based on the annotations file given. In this case the annotations file will have columns labeled organism and accession for each leaf:

visual_label: '{organism} ({accession})'

When making large trees it's sometimes a good idea to make the resulting tree image smaller by drawing some clades as cartoon wedges. These cartoon wedges can be specified using the groups key, which should contain a list where each item corresponds to a clade to be collapsed. Each list item (group) should contain a name key and an lca key. The lca key is used to specify the lowest common ancestor of a list of leaves.

groups:
    -
        name: Firmicutes
        lca:
            - leaf_1
            - leaf_2
    - 
        name: other bacteria
        lca:
            - leaf_3
            - leaf_4

Highlighting leaves can be accomplished by adding a highlight key to the configuration file. The data under this key is a list of data for each of the highlighted clades. Highlight data is required to have a color key but may then use any of the three different ways to highlight the leaves.

highlight:
    -
        color: "#FF0000"
        lca: 
            - leaf_1
            - leaf_2
    -
        color: "#00FF00"
        leaves:
            - leaf_3
            - leaf_4
    -
        color: "#0000FF"
        annotation_file:
            column: "taxonomy"
            match: "Proteobacteria"

The lca key is for highlighting an entire clade using the lowest common ancestor of a list of given leaves.

The leaves key allows you to highlight leaves that may not be monophyletic

The annotation_file key allows you specify highlighting based on the information of the csv formatted annotation file. You must provide a column key with the name of the column in the annotation file to use, and the match key which can be any valid python regular expression.