hmmalign1

Usage

Overview

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.

Options

-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.