HMMER Manual hmmalign(1) NAME hmmalign - align sequences to an HMM profile SYNOPSIS hmmalign [_o_p_t_i_o_n_s] _h_m_m_f_i_l_e _s_e_q_f_i_l_e DESCRIPTION hmmalign reads an HMM file from _h_m_m_f_i_l_e and a set of sequences from _s_e_q_f_i_l_e, aligns the sequences to the profile HMM, and outputs a multiple sequence alignment. _s_e_q_f_i_l_e may be in any unaligned or aligned file format accepted by HMMER. If it is in a multiple alignment format (e.g. Stockholm, MSF, SELEX, ClustalW), the existing align- ment is ignored (i.e., the sequences are read as if they were unaligned - hmmalign will align them the way it wants). OPTIONS -h Print brief help; includes version number and summary of all options, including expert options. -m Include in the alignment only those symbols aligned to match states. Do not show symbols assigned to insert states. -o <_f> Save alignment to file <_f> instead of to standard out- put. -q quiet; suppress all output except the alignment itself. Useful for piping or redirecting the output. EXPERT OPTIONS --informat <_s> Assert that the input _s_e_q_f_i_l_e is in format <_s>; do not run Babelfish format autodection. This increases the reliability of the program somewhat, because the Babelfish can make mistakes; particularly recommended for unattended, high-throughput runs of HMMER. Valid format strings include FASTA, GENBANK, EMBL, GCG, PIR, STOCKHOLM, SELEX, MSF, CLUSTAL, and PHYLIP. See the User's Guide for a complete list. HMMER @RELEASE@ Last change: @RELEASEDATE@ 1 HMMER Manual hmmalign(1) --mapali <_f> Reads an alignment from file <_f> and aligns it as a single object to the HMM; e.g. the alignment in <_f> is held fixed. This allows you to align sequences to a model with hmmalign and view them in the context of an existing trusted multiple alignment. The alignment to the alignment is defined by a "map" kept in the HMM, and so is fast and guaranteed to be consistent with the way the HMM was constructed from the alignment. The alignment in the file <_f> must be exactly the alignment that the HMM was built from. Compare the --withali option. --withali <_f> Reads an alignment from file <_f> and aligns it as a single object to the HMM; e.g. the alignment in <_f> is held fixed. This allows you to align sequences to a model with hmmalign and view them in the context of an existing trusted multiple alignment. The alignment to the alignment is done with a heuristic (nonoptimal) dynamic programming procedure, which may be somewhat slow and is not guaranteed to be completely consistent with the way the HMM was constructed (though it should be quite close). However, any alignment can be used, not just the alignment that the HMM was built from. Compare the --mapali option. SEE ALSO Master man page, with full list of and guide to the indivi- dual man pages: see hmmer(1). A User guide and tutorial came with the distribution: Userguide.ps [Postscript] and/or Userguide.pdf [PDF]. Finally, all documentation is also available online via WWW: http://hmmer.wustl.edu/ AUTHOR This software and documentation is: @COPYRIGHT@ HMMER - Biological sequence analysis with profile HMMs Copyright (C) 1992-1999 Washington University School of Medicine All Rights Reserved This source code is distributed under the terms of the GNU General Public License. See the files COPYING and LICENSE for details. See the file COPYING in your distribution for complete details. HMMER @RELEASE@ Last change: @RELEASEDATE@ 2 HMMER Manual hmmalign(1) Sean Eddy HHMI/Dept. of Genetics Washington Univ. School of Medicine 4566 Scott Ave. St Louis, MO 63110 USA Phone: 1-314-362-7666 FAX : 1-314-362-7855 Email: eddy@genetics.wustl.edu HMMER @RELEASE@ Last change: @RELEASEDATE@ 3