A pipeline for the following toolchain developed by AlgoLabs:
- celluloid
A tool designed to cluster single-cell-sequencing datasets that employs K-modes clustering and a novel similarity measure to better work around the uncertain data points that are frequently produced with such sequencing techniques. - sasc
A tool designed to infer phylogenies from inaccurate genotype datasets obtained using SCS techniques, that employs simulated annealing to explore the solution spaces in the k-dollo model, that better accounts for the peculiarities of cancer cell evolution without being constrainted by the infinite sites assumption. - mp3
A tool for comparisons between (potentially) fully labeled phylogenies with poly-occurring labels, with a similarity measure based on the comparison of the minimum topologies for each label triplet found in the two trees.
The pipeline also include:
- SCITE A software package to compute mutation histories of somatic cells. Given noisy mutation profiles of single cells, SCITE performs a stochastic search to find the Maximum Likelihood (ML) or Maximum aposterori (MAP) tree and/or to sample from the posterior probability distribution. Tree reconstruction can be combined with an estimation of the error rates in the mutation profiles.
- SPhyR An algorithm for reconstructing phylogenetic trees from single-cell sequencing data. SPhyR employs the k-Dollo phylogeny model, where each SNV can only be gained once but lost k times.
- [Generic] A generic algorithm to run a software not present in the list above.
In the tumor phylogeny pipeline depicted below (from https://doi.org/10.1007/978-3-031-82768-6_8), celluloid would perform step e. Mutation Clustering, sasc would perform step f. Phylogeny Inference, and mp3 would perform step h. Tree Similarity.
Note: in order to install this package, a graphviz-dev installation is required.
graphviz-dev is required to build the tool, while graphviz is required to
call PhylogenyTree.draw_to_file() and its overrides.
Once the required external software has been installed, run:
git clone https://github.com/plastic-phy/plastic.git --recurse-submodules
cd plastic
pip install .
The tool will be installed under the name plastic.
This package exposes one module, plastic and three public submodules:
plastic.treesim (mp3)
plastic.phylogeny (sasc, SCITE, SPhyR, generic)
plastic.clustering (celluloid)
That can be imported with the usual python import directives like:
from plastic import phylogeny as ph
from plastic.clustering import cluster_mutations
The three modules have been designed with the intent to closely mirror the behaviour of the three original tools while exposing them as library modules. Reading the original documentations of the tools and the documentation of the modules, which is reachable with the likes of:
from plastic import phylogeny
help(phylogeny)
will be enough to understand the usage of the modules.
Along with their main functions, the modules expose structures that are designed to easily load, store, visualize and modify the relevant datasets. Whenever structures of this kind are exposed in a module, its documentation makes mention of them, and the structures have their own documentation accessible as usual through help().