BAli-Phy version 3: Model-based co-estimation of Alignment and Phylogeny

SummaryWe describe improvements to BAli-Phy, a Markov chain Monte Carlo (MCMC) program that jointly estimates phylogeny, alignment, and other parameters from unaligned sequence data. Version 3 is substantially faster for large trees, and implements covarion models, RNA stem models, and other new models. It implements ancestral state reconstruction, allows prior selection for all model parameters, and can also analyze multiple genes simultaneously.AvailabilitySoftware is available for download at http://www.bali-phy.org. C++ source code is freely available on Github under the GPL2 [email protected]

Modeling Binary Fingerprint Descriptors With the Superposing Significant Interaction Rules (SSIR) Method

Recently, the superposing significant interaction rules (SSIR) method has been applied in several fields of QSPR to model and establish molecular rankings that correlate dichotomous properties. The origin of the method is in the field of combinatorial chemistry, but it has been shown that the procedure is fast, versatile, and that it can be applied in many other fields. In particular, an example is phospholipidosis modeling taking, as primary descriptors, the binary fingerprints of the molecules. This is the first time SSIR is used to treat this kind of descriptors. The performance achieved is similar to other results found in the literature and, in particular, to the results obtained by authors who considered the same molecular set and descriptors. One of the main advantages of SSIR is that the method acts as an automated variable selector. This allows it to be used almost immediately without prior selection of variables.