FigTree-scripts

Collection of scripts for preparing tree-files for visualisation in FigTree.

Getting started

Clone this repo

git clone https://github.com/emilhaegglund/figtree_scripts.git
cd figtree_scripts

Create new environment and install required packages using conda.

conda create env -f environment.yaml

Usage

Using the collapse_phylogeny.py script it is possible to collapse monophyletic nodes and when the output file is open in FigTree collapsed nodes will be displayed with triangles. Also, leaf and triangles will be annotated based on the given annotation file.

python collapse_phylogeny.py \
    --tree examples/collapse_phylogeny.nwk \
    --annotation examples/collapse_annotation.tsv \
    --settings examples/figtree_settings.txt \
    --column  class \
    --output collapased_phylogeny.nxs

This is an example of an annotation file with default column names. The first column is required to contain the accessions of the taxa in the phylogeny.

taxa	domain	phylum	class	order	family	genus	species
HGE70390.1	Bacteria	Poribacteria	DTPJ01	DTPJ01	DTPJ01	DTPJ01	DTPJ01 sp011334435
MBS4020802.1	Bacteria	Firmicutes_D	Dethiobacteria	Dethiobacterales	Dethiobacteraceae	JAGXRN01	JAGXRN01 sp018335875
GAB61033.1	Bacteria	Planctomycetota	Brocadiae	Brocadiales	Brocadiaceae	Jettenia	Jettenia caeni

If there are additional columns in the annotation, they will be omitted.

A custom set of columns can be defined using the --header argument with a comma-separated list of column values to use. The annotation line will be in the same order as the columns are given to the header option.

--header genus,species,strain

Coming

Scripts to color labels of a phylogeny