CMCompare: calculate the similarity between RNA families

The CMCompare algorithm calculates the similarity between two structured RNA families. The actual algorithm calculates similarity based on an underlying covariance model. At its core, CMCompare is a very specialized tree alignment algorithm.

Running CMCompare yields two principal results. First is the similarity or Link score. Second is the link sequence which belongs to the link score. The link sequence is the sequence which is most similar to both family models at the same time. I.e. the sequence which can be least discriminated. The link score is the lower of the two scores from the two models.

CMCompare returns additional information, like the columns of the alignment (model) which are most similar to each other.

README

(included from project) readme/CMCompare.md
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Installation from sources via stack:

This software can be compiled and installed using stack in a small number of steps. Note that some packages only provide a library and no executable.
  1. Prepare a directory for the software:
    mkdir ~/haskell/
    cd ~/haskell
    (If you choose another name, replace accordingly below)
  2. Install stack itself. Binaries are available here. Copy the binaries into the ~/haskell directory.
  3. Download the CMCompare software:
    ~/haskell/stack unpack CMCompare
    ls
    This unpacks the newest version of CMCompare, the version itself being referred to as -VERSION, which you should see via ls.
  4. Compile:
    cd ~/haskell/CMCompare-VERSION
    ~/haskell/stack build
  5. Execute (you can find the executable names, if any, in the cabal as executable build targets):
    ~/haskell/stack exec EXECUTABLE
  6. Optionally, install any executables into ~/haskell/bin/
    . This simplifies actually running the programs later on. mkdir -p ~/haskell/bin
    ~/haskell/stack install --local-bin-path ~/haskell/bin