Dataset Information

Clumppling: cluster matching and permutation program with integer linear programming.

ABSTRACT:

Motivation

In the mixed-membership unsupervised clustering analyses commonly used in population genetics, multiple replicate data analyses can differ in their clustering solutions. Combinatorial algorithms assist in aligning clustering outputs from multiple replicates so that clustering solutions can be interpreted and combined across replicates. Although several algorithms have been introduced, challenges exist in achieving optimal alignments and performing alignments in reasonable computation time.

Results

We present Clumppling, a method for aligning replicate solutions in mixed-membership unsupervised clustering. The method uses integer linear programming for finding optimal alignments, embedding the cluster alignment problem in standard combinatorial optimization frameworks. In example analyses, we find that it achieves solutions with preferred values of a desired objective function relative to those achieved by Pong and that it proceeds with less computation time than Clumpak. It is also the first method to permit alignments across replicates with multiple arbitrary values of the number of clusters K.

Availability and implementation

Clumppling is available at https://github.com/PopGenClustering/Clumppling.

SUBMITTER: Liu X

PROVIDER: S-EPMC10766593 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature

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Publications

Clumppling: cluster matching and permutation program with integer linear programming.

Liu Xiran X Kopelman Naama M NM Rosenberg Noah A NA

Bioinformatics (Oxford, England) 20240101 1

<h4>Motivation</h4>In the mixed-membership unsupervised clustering analyses commonly used in population genetics, multiple replicate data analyses can differ in their clustering solutions. Combinatorial algorithms assist in aligning clustering outputs from multiple replicates so that clustering solutions can be interpreted and combined across replicates. Although several algorithms have been introduced, challenges exist in achieving optimal alignments and performing alignments in reasonable comp ...[more]

PMID: 38096585

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Project description:Subspecies nomenclature systems of pathogens are increasingly based on sequence data. The use of phylogenetics to identify and differentiate between clusters of genetically similar pathogens is particularly prevalent in virology from the nomenclature of human papillomaviruses to highly pathogenic avian influenza (HPAI) H5Nx viruses. These nomenclature systems rely on absolute genetic distance thresholds to define the maximum genetic divergence tolerated between viruses designated as closely related. However, the phylogenetic clustering methods used in these nomenclature systems are limited by the arbitrariness of setting intra and intercluster diversity thresholds. The lack of a consensus ground truth to define well-delineated, meaningful phylogenetic subpopulations amplifies the difficulties in identifying an informative distance threshold. Consequently, phylogenetic clustering often becomes an exploratory, ad hoc exercise. Phylogenetic Clustering by Linear Integer Programming (PhyCLIP) was developed to provide a statistically principled phylogenetic clustering framework that negates the need for an arbitrarily defined distance threshold. Using the pairwise patristic distance distributions of an input phylogeny, PhyCLIP parameterizes the intra and intercluster divergence limits as statistical bounds in an integer linear programming model which is subsequently optimized to cluster as many sequences as possible. When applied to the hemagglutinin phylogeny of HPAI H5Nx viruses, PhyCLIP was not only able to recapitulate the current WHO/OIE/FAO H5 nomenclature system but also further delineated informative higher resolution clusters that capture geographically distinct subpopulations of viruses. PhyCLIP is pathogen-agnostic and can be generalized to a wide variety of research questions concerning the identification of biologically informative clusters in pathogen phylogenies. PhyCLIP is freely available at http://github.com/alvinxhan/PhyCLIP, last accessed March 15, 2019.

Dataset Information

Clumppling: cluster matching and permutation program with integer linear programming.

Motivation

Results

Availability and implementation

Publications

Clumppling: cluster matching and permutation program with integer linear programming.

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