This is the Windows app named Weinberg-CMfinder whose latest release can be downloaded as cmfinder-0.4.1.18.tgz. It can be run online in the free hosting provider OnWorks for workstations.
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Weinberg-CMfinder
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DESCRIPTION
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.
This is an application that can also be fetched from https://sourceforge.net/projects/weinberg-cmfinder/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
