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covariation-analysis

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Tests whether a proposed or predicted RNA secondary structure is supported by evolutionary covariation using R-scape, which scores compensatory substitutions against a phylogeny-aware null and estimates the statistical power of the alignment. Use when validating a conserved-structure claim before trusting it (the test that found no support for HOTAIR/Xist/SRA lncRNA structures); separating real covariation from phylogenetic correlation; deciding whether an alignment even has the power to test structure; or building a covariation-supported consensus (CaCoFold) to seed a covariance model or folding.

When to use

• validating a conserved-structure claim
• separating real covariation from phylogenetic correlation
• deciding whether an alignment has the power to test structure
• building a covariation-supported consensus (CaCoFold)
• seeding a covariance model or folding

When not to use

• single-sequence thermodynamic prediction

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