HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences.
BACKGROUND
Nucleotide sequence data are being produced at an ever increasing rate. Clustering such sequences by similarity is often an essential first step in their analysis-intended to reduce redundancy, define gene families or suggest taxonomic units. Exact clustering algorithms, such as hierarchical clustering, scale relatively poorly in terms of run time and memory usage, yet they are desirable because heuristic shortcuts taken during clustering might have unintended consequences in later analysis steps.


RESULTS
Here we present HPC-CLUST, a highly optimized software pipeline that can cluster large numbers of pre-aligned DNA sequences by running on distributed computing hardware. It allocates both memory and computing resources efficiently, and can process more than a million sequences in a few hours on a small cluster.


METHODS
Source code and binaries are freely available at http://meringlab.org/software/hpc-clust/; the pipeline is implemented in Cþþ and uses the Message Passing Interface (MPI) standard for distributed computing.
Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland.
João F
JF
Matias Rodrigues
Christian
C
von Mering
D000465:Algorithms; D016000:Cluster Analysis; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S