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An algorithm for hierarchical clustering analysis of massive sequence data. To avoid confusion, we note that ESPRIT-Tree is not a program for determining phylogenetic trees, but rather for producing hierarchical clusters of sequences based on sequence similarity, using a tree-like data structure. We extended the concept of space partition used by previous methods for handling sequence data of varying lengths. By assuming that sequence data lives in a pseudometric space, we created a distance-based partition of the data without explicitly defining an inner-product operator to divide the space, and organized the partition results in a pseudometric based partition tree. By repeatedly applying the triangular inequality, a fast closest-pair searching algorithm was developed within the ESPRIT-Tree framework. An efficient method for dynamic insertion and deletion of tree nodes were also developed.

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ESPRIT-Tree classification

ESPRIT-Tree specifications

Unique identifier:
OMICS_01445
Interface:
Command line interface
Operating system:
Unix/Linux
Stability:
Stable
Software type:
Package/Module
Restrictions to use:
None
Computer skills:
Advanced
Maintained:
Yes

ESPRIT-Tree distribution

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No versioning.

Credits

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Publications

Institution(s)

Interdisciplinary Center for Biotechnology Research University of Florida, Gainesville, FL, USA

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