tree_annot
Simple program for creating an image of a phylogenetic tree coloured by a user-provided annotations file.
User provides -
-
A phylogenetic tree
-
An alignment file
-
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.
Installation
Currently this is just provided as a Python script. Easiest way to use it right now is -
- Clone this repository to your desktop
git clone https://github.com/gabefoley/tree_annot.git
- Install the required Python modules as specified in requirements.txt (we assume Python>=3.5)
pip install -r requirements.txt
Usage
Basic usage
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
Specify out path
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
Specifying the colour scheme
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