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Our models and model selection methods are freely available in the open-source PHASE 3.0 software.

All methods are freely available as open-source software from the authors.

While most of the newly developed methods are freely available, their use requires substantial computational skills.

Many of these methods are freely available through the internet, however, few standalone implementations are available.

Whenever available, implementations and algorithms of our methods are freely available from the CRAN consortium (Comprehensive R Archive Network) at http://cran.r-project.org/.org/

Three of the four methods are freely available implementations, while the fourth was developed within the project and is included in CASE's source code.

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A software package implementing our methods is freely available at http://bogdan.bioinformatics.ucla.edu/software/.ucla.edu/software/

The PHYLIP package was used because it offers many different analysis methods, is freely available and is commonly used [ 44].

Software to simulate transcript sets, expression values and sequence reads under a wider range of parameter values and to compare sensitivity, precision and signal-to-noise ratios of different methods is freely available online (https://github.com/boboppie/RSSS) and can be expanded by interested parties to include methods other than the exemplars presented in this article.

The proposed method is freely available as a web service at http://www.way2drug.com/RA/.

The software employing this method is freely accessible from http://www.p-graph.com/pnsstudio, TU Graz [9].

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