Metadata-Version: 2.1
Name: LAML
Version: 0.0.2
Summary: LAML: Lineage Analysis via Maximum Likelihood
Author: ['Uyen Mai', 'Gillian Chu', 'Ben Raphael']
License: GNU General Public License, version 3
Keywords: Phylogenetics Evolution Computational Maximum-likelihood Lineage Tracing
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License (GPL)
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
License-File: LICENSE
Requires-Dist: scipy >=1.3.1
Requires-Dist: cvxpy >=1.4
Requires-Dist: treeswift >=1.1.39
Requires-Dist: Mosek >=10.1.16
Requires-Dist: setuptools

LAML is a maximum likelihood algorithm under the Probabilistic Mixed-type Missing (PMM) model. Given a lineage tracing experiment character matrix with heterogeneous per-site alphabets and mutation probabilities, LAML will find a maximum likelihood tree topology and estimate branch lengths as well as stochastic dropout and heritable silencing missing data rates.