hmmalign - align sequences to a profile
hmmalign [options] hmmfile seqfile
Perform a multiple sequence alignment of all the sequences in
seqfile by aligning them individually to the profile HMM in
hmmfile. The new alignment is output to stdout.
The hmmfile should contain only a single profile. If it
contains more, only the first profile in the file will be used.
Either hmmfile or seqfile (but not both) may be '-'
(dash), which means reading this input from stdin rather than a file.
The sequences in seqfile are aligned in unihit local
alignment mode. Therefore they should already be known to contain only a
single domain (or a fragment of one). The optimal alignment may assign some
residues as nonhomologous (N and C states), in which case these residues are
still included in the resulting alignment, but shoved to the outer edges. To
trim these unaligned nonhomologous residues from the result, see the
--trim option.
- -h
- Help; print a brief reminder of command line usage and all available
options.
- -o <f>
- Direct the output alignment to file <f>, rather than to
stdout.
- --mapali
<f>
- Merge the existing alignment in file <f> into the result,
where <f> is exactly the same alignment that was used to
build the model in hmmfile. This is done using a map of alignment
columns to consensus profile positions that is stored in the
hmmfile. The multiple alignment in <f> will be exactly
reproduced in its consensus columns (as defined by the profile), but the
displayed alignment in insert columns may be altered, because insertions
relative to a profile are considered by convention to be unaligned data.
- --trim
- Trim nonhomologous residues (assigned to N and C states in the optimal
alignments) from the resulting multiple alignment output.
- --amino
- Assert that sequences in seqfile are protein, bypassing alphabet
autodetection.
- --dna
- Assert that sequences in seqfile are DNA, bypassing alphabet
autodetection.
- --rna
- Assert that sequences in seqfile are RNA, bypassing alphabet
autodetection.
- --informat
<s>
- Assert that input seqfile is in format <s>, bypassing
format autodetection. Common choices for <s> include:
fasta, embl, genbank. Alignment formats also work;
common choices include: stockholm, a2m, afa,
psiblast, clustal, phylip. For more information, and
for codes for some less common formats, see main documentation. The string
<s> is case-insensitive (fasta or FASTA both
work).
- --outformat
<s>
- Write the output alignment in format <s>. Common choices for
<s> include: stockholm, a2m, afa,
psiblast, clustal, phylip. The string
<s> is case-insensitive (a2m or A2M both work).
Default is stockholm.
See hmmer(1) for a master man page with a list of all the
individual man pages for programs in the HMMER package.
For complete documentation, see the user guide that came with your
HMMER distribution (Userguide.pdf); or see the HMMER web page
(http://hmmer.org/).
Copyright (C) 2020 Howard Hughes Medical Institute.
Freely distributed under the BSD open source license.
For additional information on copyright and licensing, see the
file called COPYRIGHT in your HMMER source distribution, or see the HMMER
web page (http://hmmer.org/).