Simple program for creating an image of a phylogenetic tree coloured by a user-provided annotations file.

User provides -

1. A phylogenetic tree

2. An alignment file

3. A csv file where the first column is a list of sequence names called Name and the next columns can be any categorical information

The user then selects which column they wish to colour on and a filename to write the image to.

Currently this is just provided as a Python script. Easiest way to use it right now is -

1. Clone this repository to your desktop

git clone https://github.com/gabefoley/tree_annot.git

2. Install the required Python modules as specified in requirements.txt (we assume Python>=3.5)

pip install -r requirements.txt

usage: tree_annot.py [-h] -t TREE -a ALIGN -c CSV -col COL [-r RANDOM_SEED]
                     [-o OUTPATH]

You can call tree_annot from the command line.

The paths to the tree, alignment, csv file, and the column to annotate based on must be provided.

python tree_annot.py -t ./examples/CYP2U_165.nwk -a ./examples/CYP2U_165.aln -c ./examples/CYP2U_165.csv -col tag1

Example files showing expected format of all three are given in the examples folder

The alignment file can be an alignment with or without ancestral sequences

By default the image is written to a file called tree_annot.png.

Change this by using the -o flag

python tree_annot.py -t ./examples/CYP2U_165.nwk -a ./examples/CYP2U_165.aln 
-c ./examples/CYP2U_165.csv -col tag1 -o ./examples/changed_name.png

If you don't set a random seed, the colours will be automatically chosen for you (using a method designed to give contrasting colours). When the program runs, it will tell you the random seed used to generate the colour scheme

To reproduce this colour scheme set the random seed as 90

You can then provide this number to tree_annot using the -r flag to use this colour scheme

python tree_annot.py -t ./examples/CYP2U_165.nwk -a ./examples/CYP2U_165.aln 
-c ./examples/CYP2U_165.csv -col "tag2" -r 90