hhconsensus(1) [debian man page]
HHCONSENSUS(1) User Commands HHCONSENSUS(1) NAME
hhconsensus - calculate the consensus sequence for an A3M/FASTA input file SYNOPSIS
hhconsensus -i <file> [options] DESCRIPTION
HHconsensus version 2.0.15 (June 2012) Calculate the consensus sequence for an A3M/FASTA input file. (C) Johannes Soeding, Michael Rem- mert, Andreas Biegert, Andreas Hauser Remmert M, Biegert A, Hauser A, and Soding J. HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat. Methods 9:173-175 (2011). -i <file> query alignment (A2M, A3M, or FASTA), or query HMM Output options: -s <file> append consensus sequence in FASTA (default=<infile.seq>) -o <file> write alignment with consensus sequence in A3M -oa3m <file> same -oa2m <file> write alignment with consensus sequence in A2M -ofas <file> write alignment with consensus sequence in FASTA -v <int> verbose mode: 0:no screen output 1:only warings 2: verbose Filter input alignment (options can be combined): -id [0,100] maximum pairwise sequence identity (%) (def=100) -diff [0,inf[ filter most diverse set of sequences, keeping at least this many sequences in each block of >50 columns (def=0) -cov [0,100] minimum coverage with query (%) (def=0) -qid [0,100] minimum sequence identity with query (%) (def=0) -qsc [0,100] minimum score per column with query (def=-20.0) Input alignment format: -M a2m use A2M/A3M (default): upper case = Match; lower case = Insert; '-' = Delete; '.' = gaps aligned to inserts (may be omitted) -M first use FASTA: columns with residue in 1st sequence are match states -M [0,100] use FASTA: columns with fewer than X% gaps are match states Other options: -addss add predicted secondary structure information from PSIPRED Example: hhconsensus -i stdin -s stdout hhconsensus 2.0.15 June 2012 HHCONSENSUS(1)
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cmemit(1) Infernal Manual cmemit(1) NAME
cmemit - generate sequences from a covariance model SYNOPSIS
cmemit [options] cmfile seqfile DESCRIPTION
cmemit reads the covariance model(s) (CMs) in cmfile and generates a number of sequences from the CM(s); or if the -c option is selected, generates a single majority-rule consensus. This can be useful for various application in which one needs a simulation of sequences consis- tent with a sequence family consensus. By default, cmemit generates 10 sequences and outputs them in FASTA (unaligned) format to seqfile. GENERAL OPTIONS
-h Print brief help; includes version number and summary of all options, including expert options. -o <f> Save the synthetic sequences to file <f> rather than writing them to stdout. -n <n> Generate <n> sequences. Default is 10. -u Write the generated sequences in unaligned format (FASTA). This is the default, so this option is probably useless. -a Write the generated sequences in an aligned format (STOCKHOLM) with consensus structure annotation rather than FASTA. -c Predict a single majority-rule consensus sequence instead of sampling sequences from the CM's probability distribution. Highly con- served residues (base paired residues that score higher than 3.0 bits, or single stranded residues that score higher than 1.0 bits) are shown in upper case; others are shown in lower case. -l Configure the CMs into local mode before emitting sequences. See the User's Guide for more information on locally configured CMs. -s <n> Set the random seed to <n>, where <n> is a positive integer. The default is to use time() to generate a different seed for each run, which means that two different runs of cmemit on the same CM will give different results. You can use this option to generate repro- ducible results. --devhelp Print help, as with -h , but also include undocumented developer options. These options are not listed below, are under development or experimental, and are not guaranteed to even work correctly. Use developer options at your own risk. The only resources for understanding what they actually do are the brief one-line description printed when --devhelp is enabled, and the source code. EXPERT OPTIONS
--rna Specify that the emitted sequences be output as RNA sequences. This is true by default. --dna Specify that the emitted sequences be output as DNA sequences. By default, the output alphabet is RNA. --tfile <f> Dump tabular sequence parsetrees (tracebacks) for each emitted sequence to file <f>. Primarily useful for debugging. --exp <x> Exponentiate the emission and transition probabilities of the CM by <x> and then renormalize those distributions before emitting sequences. This option changes the CM probability distribution of parsetrees relative to default. With <x> less than 1.0 the emitted sequences will tend to have lower bit scores upon alignment to the CM with cmalign. With <x> greater than 1.0, the emitted sequences will tend to have higher bit scores upon alignment to the CM. This bit score difference will increase as <x> moves further away from 1.0 in either direction. If <x> equals 1.0, this option has no effect relative to default. This option is useful for generating sequences that are either difficult ( <x> < 1.0) or easy ( <x> > 1.0) for the CM to distinguish as homologous from back- ground, random sequence. --begin <n> Truncate the resulting alignment by removing all residues before consensus column <n>, where <n> is a positive integer no greater than the consensus length of the CM. Must be used in combination with --end and either -a or --shmm (a developer option). --end <n> Truncate the resulting alignment by removing all residues after consensus column <n>, where <n> is a positive integer no greater than the consensus length of the CM. Must be used in combination with --begin and either -a or --shmm (a developer option). SEE ALSO
For complete documentation, see the User's Guide (Userguide.pdf) that came with the distribution; or see the Infernal web page, http://infernal.janelia.org/. COPYRIGHT
Copyright (C) 2009 HHMI Janelia Farm Research Campus. Freely distributed under the GNU General Public License (GPLv3). See the file COPYING that came with the source for details on redistribution conditions. AUTHOR
Eric Nawrocki, Diana Kolbe, and Sean Eddy HHMI Janelia Farm Research Campus 19700 Helix Drive Ashburn VA 20147 http://selab.janelia.org/ Infernal 1.0.2 October 2009 cmemit(1)