This is the command hmmalign that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
hmmalign - align sequences to a profile HMM
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 in
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
-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.
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.
Specify that all sequences in <seqfile> are proteins. By default, alphabet type is
autodetected from looking at the residue composition.
--dna Specify that all sequences in <seqfile> are DNAs.
--rna Specify that all sequences in <seqfile> are RNAs.
Declare that the input <seqfile> is in format <s>. Accepted sequence file formats
include FASTA, EMBL, GenBank, DDBJ, UniProt, Stockholm, and SELEX. Default is to
autodetect the format of the file.
Specify that the output multiple alignment is in format <s>. Currently the
accepted multiple alignment sequence file formats only include Stockholm and SELEX.
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