HMMER User’s Guide - Eddy Lab

HMMER user 's Guide Biological sequence analysis using profile hidden Markov models Version ; February 2015. Sean R. Eddy, Travis J. Wheeler and the HMMER development team Copyright (C) 2015 Howard Hughes Medical Institute. Permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and this permission notice are retained on all copies. HMMER is licensed and freely distributed under the GNU General Public License version 3 (GPLv3). For a copy of the License, see HMMER is a trademark of the Howard Hughes Medical Institute. 1. Contents 1 Introduction 7. How to avoid reading this manual .. 7. How to avoid using this software (links to similar software) .. 7. What profile HMMs are .. 7. Applications of profile HMMs .. 8. Design goals of HMMER3 .. 9. What's new in .. 10. What's still missing in .. 11. How to learn more about profile HMMs .. 11. 2 Installation 13. Quick installation instructions .. 13. System requirements .. 13. Multithreaded parallelization for multicores is the default.

HMMER is used to search sequence databases for homologs of protein or DNA sequences, and to make sequence alignments. HMMER can be used to search sequence databases with single query sequences but it becomes particularly powerful when the query is an alignment of multiple instances of a sequence family.

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