Provided by: hmmer_3.1b2-2_amd64 
NAME
alimask - Add mask line to a multiple sequence alignment
SYNOPSIS
alimask [options] <msafile> <postmsafile>
DESCRIPTION
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.
OPTIONS
-h 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.
OPTIONS FOR SPECIFYING MASK RANGE
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.
--modelrange <s>
Supply the given range(s) in model coordinates.
--alirange <s>
Supply the given range(s) in alignment coordinates.
--apendmask
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).
OPTIONS FOR SPECIFYING THE ALPHABET
The alphabet type (amino, DNA, or RNA) is autodetected by default, by looking at the composition of the
msafile. Autodetection is normally quite reliable, but occasionally alphabet type may be ambiguous and
autodetection can fail (for instance, on tiny toy alignments of just a few residues). To avoid this, or
to increase robustness in automated analysis pipelines, you may specify the alphabet type of msafile with
these options.
--amino
Specify that all sequences in msafile are proteins.
--dna Specify that all sequences in msafile are DNAs.
--rna Specify that all sequences in msafile are RNAs.
OPTIONS CONTROLLING PROFILE CONSTRUCTION
These options control how consensus columns are defined in an alignment.
--fast 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.
--hand 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 --fragthresh0 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
--fragthresh1 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.
OPTIONS CONTROLLING RELATIVE WEIGHTS
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.
--wpb Use the Henikoff position-based sequence weighting scheme [Henikoff and Henikoff, J. Mol. Biol.
243:574, 1994]. This is the default.
--wgsc Use the Gerstein/Sonnhammer/Chothia weighting algorithm [Gerstein et al, J. Mol. Biol. 235:1067,
1994].
--wblosum
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.
--wnone
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.
OTHER OPTIONS
--informat <s>
Declare that the input msafile is in format <s>. Currently the accepted multiple alignment
sequence file formats include Stockholm, Aligned FASTA, Clustal, NCBI PSI-BLAST, PHYLIP, Selex,
and UCSC SAM A2M. Default is to autodetect the format of the file.
--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 ALSO
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
Copyright (C) 2015 Howard Hughes Medical Institute.
Freely distributed under the GNU General Public License (GPLv3).
For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source
distribution, or see the HMMER web page ().
AUTHOR
Eddy/Rivas Laboratory
Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147 USA
http://eddylab.org
HMMER 3.1b2 February 2015 alimask(1)