Weinberg-CMfinder

The CMfinder package is a suite of programs with two main purposes:

(1) the cmfinder program infers an alignment and consensus secondary structure of an RNA, using unaligned sequences as input.

(2) other tools score alignments to indicate evidence of RNA secondary structure within the alignment. RNAphylo assigns a probabilistic score to an existing alignment, using an explicit phylogenetic model. hmmpair assigns a score based on evidence of covariation that is supported by sequence conservation. The ScoreMotif.pl script combines these two scores into one.

CMfinder 0.4.1 was written by Zasha Weinberg, based on the CMfinder 0.3 package by Zizhen Yao, Infernal 1.1 by Eric Nawrocki and Sean Eddy, and others. The main differences of CMfinder 0.4.1 are handling truncated metagenomic sequences, integration of infernal 1.1 and the hmmpair program.

See the Wiki for additional information, and citations.