cmpress(1) | Infernal Manual | cmpress(1) |
cmpress - prepare a covariance model database for cmscan
cmpress [options] <cmfile>
Starting from a CM database <cmfile> in standard Infernal-1.1 format, construct binary compressed datafiles for cmscan. The cmpress step is required for cmscan to work.
The <cmfile> must be have already been calibrated with cmcalibrate for cmpress to work.
Four files are created: <cmfile>.i1m, <cmfile>.i1i, <cmfile>.i1f, and <cmfile>.i1p. The <cmfile>.i1m file contains the covariance models, associated filter p7 profile HMMs and their annotation in a binary format. The <cmfile>.i1i file is an SSI index for the <cmfile>.i1m file. The <cmfile>.i1f file contains precomputed data structures for the fast heuristic filter (the SSV filter) for the filter p7 profile HMMs in <cmfile>. The <cmfile>.i1p file contains precomputed data structures for the rest of each profile filter p7 HMM.
<cmfile> may not be '-' (dash); running cmpress on a standard input stream rather than a file is not allowed.
See infernal(1) for a master man page with a list of all the individual man pages for programs in the Infernal package.
For complete documentation, see the user guide that came with your Infernal distribution (Userguide.pdf); or see the Infernal web page ().
Copyright (C) 2016 Howard Hughes Medical Institute. Freely distributed under a BSD open source license.
For additional information on copyright and licensing, see the file called COPYRIGHT in your Infernal source distribution, or see the Infernal web page ().
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July 2016 | Infernal 1.1.2 |