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Release 1.0.2
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A few minor changes and bug fixes:
- simScore() now calculates the area under the ROC curve as well. It now takes as input an align object and a cosmo object.
- rseq() can now simulate sequences of variable lenghts.
- The cosmo class now includes a slot of class align that ranks all potential start sites by posterior probability.
- The readFASTA() function (not exported) now closes any connection that was opened during the call.
- The example file seq.fasta now contains 10 rather than 20 sequences to make the vignette less bulky.
- The package now uses a CITATION file instead of the citation.cosmo() function.
- Global variables created by the constraint GUI are removed on exit.
- A minor bug in the selection of the order of the background model was fixed. The bug occurred with some datasets that contained unknown characters like 'N' or 'X'.
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Release 1.0.1
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A few minor changes and bug fixes:
- If the datasets contains only one sequence, only the TCM model will be considered. A 0th order Markov model is used for the background distribution. All other model parameters are selected based on the E-value by default.
- The TCM model does not report overlapping motifs anymore.
- A minor bug in creating the sel.model output slot was fixed.
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Release 1.0.0
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Initial release.