treesumstats 0.1

Encoding phylogenetic trees with summary statistics.

treesumstats

Representing phylogenetic trees (or forests of such trees) as summary statistics.

Implemented summary statistics

Input data

One needs to supply a time-scaled phylogenetic tree in newick format. If the file contains several trees (one tree per line), it will be considered as a forest.

Installation

There are 4 alternative ways to run treesumstats on your computer: with docker, apptainer, in Python3, or via command line (requires installation with Python3).

Run in python3 or command-line (for linux systems, recommended Ubuntu 21 or newer versions)

You could either install python (version 3.9 or higher) system-wide and then install treesumstats via pip:

sudo apt install -y python3 python3-pip python3-setuptools python3-distutils
pip3 install treesumstats

or alternatively, you could install python (version 3.9 or higher) and treesumstats via conda (make sure that conda is installed first). Here we will create a conda environment called phyloenv:

conda create --name phyloenv python=3.9
conda activate phyloenv
pip install treesumstats

Basic usage in a command line

If you installed treesumstats in a conda environment (here named phyloenv), do not forget to first activate it, e.g.

conda activate phyloenv

Run the following command to calculate the summary statistics for an input tree tree.nwk and save them to an output tab-delimited file stats.tab. (The non-mandatory option --add_descriptions would add a column with statistics descriptions to the output table.)

treesumstats_encode --nwk tree.nwk --tab stats.tab --add_descriptions

Help

To see detailed options, run:

treesumstats_encode --help

Run with docker

Basic usage

Once docker is installed,

run the following command to calculate the summary statistics for an input tree tree.nwk and save them to an output tab-delimited file stats.tab. (The non-mandatory option --add_descriptions would add a column with statistics descriptions to the output table.)

docker run -v <path_to_the_folder_containing_the_tree>:/data:rw -t evolbioinfo/treesumstats --nwk /data/tree.nwk --tab /data/stats.tab --add_descriptions

This will produce a tab-delimited file stats.tab in the <path_to_the_folder_containing_the_tree> folder,

containing the summary statistic names in the statistic column, their values in the value column and their descriptions in the description column.

Help

To see advanced options, run

docker run -t evolbioinfo/treesumstats -h

Run with apptainer

Basic usage

Once apptainer is installed,

run the following command to calculate the summary statistics for an input tree tree.nwk and save them to an output tab-delimited file stats.tab. (The non-mandatory option --add_descriptions would add a column with statistics descriptions to the output table.)

apptainer run docker://evolbioinfo/treesumstats --nwk tree.nwk --tab stats.tab --add_descriptions

This will produce a tab-delimited file stats.tab,

containing the summary statistic names in the statistic column, their values in the value column and their descriptions in the description column.

Help

To see advanced options, run

apptainer run docker://evolbioinfo/treesumstats -h