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alimask - calculate and add column mask to a multiple sequence alignment


alimask [options] msafile postmsafile


alimask is used to apply a mask line to a multiple sequence alignment, based on provided alignment or model coordinates. When hmmbuild receives a masked alignment as input, it produces a profile model in which the emission probabilities at masked positions are set to match the background frequency, rather than being set based on observed frequencies in the alignment. Position-specific insertion and deletion rates are not altered, even in masked regions. alimask autodetects input format, and produces masked alignments in Stockholm format. msafile may contain only one sequence alignment.

A common motivation for masking a region in an alignment is that the region contains a simple tandem repeat that is observed to cause an unacceptably high rate of false positive hits.

In the simplest case, a mask range is given in coordinates relative to the input alignment, using --alirange <s>. However it is more often the case that the region to be masked has been identified in coordinates relative to the profile model (e.g. based on recognizing a simple repeat pattern in false hit alignments or in the HMM logo). Not all alignment columns are converted to match state positions in the profile (see the --symfrac flag for hmmbuild for discussion), so model positions do not necessarily match up to alignment column positions. To remove the burden of converting model positions to alignment positions, alimask accepts the mask range input in model coordinates as well, using --modelrange <s>. When using this flag, alimask determines which alignment positions would be identified by hmmbuild as match states, a process that requires that all hmmbuild flags impacting that decision be supplied to alimask. It is for this reason that many of the hmmbuild flags are also used by alimask.



Help; print a brief reminder of command line usage and all available options.

-o <f>

Direct the summary output to file <f>, rather than to stdout.


A single mask range is given as a dash-separated pair, like --modelrange 10-20 and multiple ranges may be submitted as a comma-separated list, --modelrange 10-20,30-42.

Supply the given range(s) in model coordinates.

--alirange <s>

Supply the given range(s) in alignment coordinates.


Add to the existing mask found with the alignment. The default is to overwrite any existing mask.

--model2ali <s>

Rather than actually produce the masked alignment, simply print model range(s) corresponding to input alignment range(s).

--ali2model <s>

Rather than actually produce the masked alignment, simply print alignment range(s) corresponding to input model range(s).



Assert that sequences in msafile are protein, bypassing alphabet autodetection.


Assert that sequences in msafile are DNA, bypassing alphabet autodetection.


Assert that sequences in msafile are RNA, bypassing alphabet autodetection.


These options control how consensus columns are defined in an alignment.


Define consensus columns as those that have a fraction >= symfrac of residues as opposed to gaps. (See below for the --symfrac option.) This is the default.


Define consensus columns in next profile using reference annotation to the multiple alignment. This allows you to define any consensus columns you like.

--symfrac <x>

Define the residue fraction threshold necessary to define a consensus column when using the --fast option. The default is 0.5. The symbol fraction in each column is calculated after taking relative sequence weighting into account, and ignoring gap characters corresponding to ends of sequence fragments (as opposed to internal insertions/deletions). Setting this to 0.0 means that every alignment column will be assigned as consensus, which may be useful in some cases. Setting it to 1.0 means that only columns that include 0 gaps (internal insertions/deletions) will be assigned as consensus.

--fragthresh <x>

We only want to count terminal gaps as deletions if the aligned sequence is known to be full-length, not if it is a fragment (for instance, because only part of it was sequenced). HMMER uses a simple rule to infer fragments: if the sequence length L is less than or equal to a fraction <x> times the alignment length in columns, then the sequence is handled as a fragment. The default is 0.5. Setting --fragthresh 0 will define no (nonempty) sequence as a fragment; you might want to do this if you know you’ve got a carefully curated alignment of full-length sequences. Setting --fragthresh 1 will define all sequences as fragments; you might want to do this if you know your alignment is entirely composed of fragments, such as translated short reads in metagenomic shotgun data.


HMMER uses an ad hoc sequence weighting algorithm to downweight closely related sequences and upweight distantly related ones. This has the effect of making models less biased by uneven phylogenetic representation. For example, two identical sequences would typically each receive half the weight that one sequence would. These options control which algorithm gets used.


Use the Henikoff position-based sequence weighting scheme [Henikoff and Henikoff, J. Mol. Biol. 243:574, 1994]. This is the default.


Use the Gerstein/Sonnhammer/Chothia weighting algorithm [Gerstein et al, J. Mol. Biol. 235:1067, 1994].


Use the same clustering scheme that was used to weight data in calculating BLOSUM subsitution matrices [Henikoff and Henikoff, Proc. Natl. Acad. Sci 89:10915, 1992]. Sequences are single-linkage clustered at an identity threshold (default 0.62; see --wid) and within each cluster of c sequences, each sequence gets relative weight 1/c.


No relative weights. All sequences are assigned uniform weight.

--wid <x>

Sets the identity threshold used by single-linkage clustering when using --wblosum. Invalid with any other weighting scheme. Default is 0.62.


--informat <s>

Assert that input msafile is in alignment format <s>, bypassing format autodetection. Common choices for <s> 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 (a2m or A2M both work).

--outformat <s>

Write the output postmsafile in alignment 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.

--seed <n>

Seed the random number generator with <n>, an integer >= 0. If <n> is nonzero, any stochastic simulations will be reproducible; the same command will give the same results. If <n> is 0, the random number generator is seeded arbitrarily, and stochastic simulations will vary from run to run of the same command. The default seed is 42.


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 (


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 (