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The CMfinder package amounts random suite of programs with two major purposes: (1) the cmfinder strategy infers this alignment and synergy secondary structure of an RNA, using unaligned sequences as input. (2) other tools score alignments to indicate evidence of RNA secondary structure within the interconnection. RNAphylo assigns a probabilistic score to an existing alignment, using an explicit phylogenetic mockup. hmmpair hands out a score premised on evidence of covariation who is supported through the use of sequence conservation. The ScoreMotif.pl script combines these two scores into one. CMfinder 0.4.1 represented written throughout Zasha Weinberg, underpinned on the CMfinder 0.3 package by Zizhen Yao, Infernal 1.1 by Eric Nawrocki and Sean Eddy, and others. The main separation of CMfinder 0.4.1 exist as handling truncated metagenomic sequences, integration of infernal 1.1 as well the hmmpair program. See his Wiki for additional information, and citations.

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