hmmstat(1) [debian man page]
hmmstat(1) HMMER Manual hmmstat(1) NAME
hmmstat - display summary statistics for a profile file SYNOPSIS
hmmstat [options] <hmmfile> DESCRIPTION
The hmmstat utility prints out a tabular file of summary statistics for each profile in <hmmfile>. The columns are: idx The index of this profile, numbering each on in the file starting from 1. name The name of the profile. accession The optional accession of the profile, or "-" if there is none. nseq The number of sequences that the profile was estimated from. eff_nseq The effective number of sequences that the profile was estimated from, after HMMER applied an effective sequence number calculation such as the default entropy weighting. M The length of the model in consensus residues (match states). relent Mean relative entropy per match state, in bits. This is the expected (mean) score per consensus position. This is what the default entropy-weighting method for effective sequence number estimation focuses on, so for default HMMER3 models, you expect this value to reflect the default target for entropy-weighting. info Mean information content per match state, in bits. Probably not useful. Information content is a slightly different calculation than relative entropy. p relE Mean positional relative entropy, in bits. This is a fancier version of the per-match-state relative entropy, taking into account the transition (insertion/deletion) probabilities; it may be a more accurate estimation of the average score contributed per model consensus position. compKL Kullback-Leibler distance between the model's overall average residue composition and the default background frequency distribution. The higher this number, the more biased the residue composition of the profile is. Highly biased profiles can slow the HMMER3 accel- eration pipeline, by causing too many nonhomologous sequences to pass the filters. OPTIONS
-h Help; print a brief reminder of command line usage and all available options. 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 (@HMMER_URL@). COPYRIGHT
@HMMER_COPYRIGHT@ p@HMMER_LICENSE@ For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER web page (@HMMER_URL@). AUTHOR
Eddy/Rivas Laboratory Janelia Farm Research Campus 19700 Helix Drive Ashburn VA 20147 USA http://eddylab.org HMMER
@HMMER_VERSION@ @HMMER_DATE@ hmmstat(1)
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hmmalign(1) HMMER Manual hmmalign(1) NAME
hmmalign - align sequences to a profile HMM SYNOPSIS
hmmalign [options] <hmmfile> <seqfile> DESCRIPTION
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 Stockholm format. The sequences in seqfile are aligned in unihit local alignment mode. Therefore they should already be known to contain a single domain; they should not contain more than one domain. They may be fragments. 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 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. --allcol Include columns in the output alignment for every match (consensus) state in the hmmfile, even if it means having all-gap columns. This is useful in analysis pipelines that need to be able to maintain a predetermined profile HMM architecture (with an unchanging number of consensus columns) through an hmmalign step. --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 multi- ple 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 Specify that all sequences in seqfile are proteins. By default, alphabet type is autodetected from looking at the residue composi- tion. --dna Specify that all sequences in seqfile are DNAs. --rna Specify that all sequences in seqfile are RNAs. --informat <s> Declare that the input seqfile is in format <s>. Accepted sequence file formats include FASTA, EMBL, Genbank, DDBJ, Uniprot, Stock- holm, and SELEX. Default is to autodetect the format of the file. --outformat <s> Specify that the msafile is in format <s>. Currently the accepted multiple alignment sequence file formats only include Stockholm and SELEX. Default is to autodetect the format of the file. 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 (@HMMER_URL@). COPYRIGHT
@HMMER_COPYRIGHT@ @HMMER_LICENSE@ For additional information on copyright and licensing, see the file called COPYRIGHT in your HMMER source distribution, or see the HMMER web page (@HMMER_URL@). AUTHOR
Eddy/Rivas Laboratory Janelia Farm Research Campus 19700 Helix Drive Ashburn VA 20147 USA http://eddylab.org HMMER
@HMMER_VERSION@ @HMMER_DATE@ hmmalign(1)