Hmmbuild manual

We believe HMMER compiles and runs on any POSIX-compliant system with an ANSI C99 compiler, including Mac OS/X, Linux, and any UNIX operating systems, provided it supports SSE2 or big-endian Altivec/VMX vector instructions. This includes essentially all Intel/AMD compatible machines and some PowerPC machines. hmmer user’s guide 5 hmmscan - search sequence(s) against a profile database 98 hmmsearch - search profile(s) against a sequence. Contents 1 Introduction 7 How to avoid reading this manual 7 How to avoid using this File Size: KB.

hmmbuild - Man Page. construct profile HMM(s) from multiple sequence alignment(s) Synopsis. hmmbuild [options] Description. For each multiple sequence alignment in build a profile HMM and save it to a new file. may be '-' (dash), which means reading this input from stdin rather than a file. HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). HMMER is often used together with a profile database, such as Pfam or many of the databases that participate in Interpro. hmmcalibrate - calibrate HMM search statistics. Synopsis hmmcalibrate [options] hmmfile. Description. hmmcalibrate reads an HMM file from hmmfile, scores a large number of synthesized random sequences with it, fits an extreme value distribution (EVD) to the histogram of those scores, and re-saves hmmfile now including the EVD parameters.

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