Identify phylogenetically close pairs of proteomes, located in different partitions across the phylogenetic tree.
Documentation can be found here
Phylabelle is basically a pipeline, for the identification of phylogenetically close pairs of oppositely labeled proteomes in a phylogenetic tree. It comes with an example project, containing labels and a tree for pathogenic and non-pathogenic bacteria.
There are two purposes, one can use phylabelle for:
- obtain pairs from the example project, i.e. find out pairs of closely related pathogenic and non-pathogenic bacteria
- given labels, indicating some other bacterial feature, phylabelle can be used for the complete process: automatic download of proteomes, construction of phylogeny and finally obtaining of pairs.
To obtain the installation files just download the zip from https://github.com/knthls/phylabelle or if you prefer using git just enter
git clone https://github.com/knthls/phylabelle.git
in a terminal window. Then move to phylabelles root directory and install it with
python setup.py install
If the installation fails because of lxml (e.g. because you're trying to install phylabelle in a virtual environment) try it with libxml2-dev and libxslt-dev installed.
apt-get install libxml2-dev libxslt-dev
If you intend to construct your own phylogeny, taking advadntage of the built in wrapper for PhyloPhlAn, make sure PhyloPhlAn is installed and working. (see https://huttenhower.sph.harvard.edu/phylophlan or check out the tutorial here)
In case you need to install phylabelle locally, just use
python setup.py install --user
and make sure, that ~/.local/bin is part of your $PATH-Variable.