Brooks Parsimony Analysis is a cladistic biogeographic method that aims to extract biogeographic information from phylogenetic trees, depicting from a group of cladograms a general pattern of relationships among the areas the taxa inhabit. We present here BuM 2.0, an online framework to automatically create matrices for Brooks Parsimony Analysis (BPA) using Baum & Ragan’s algorithm for Matrix Representation with Parsimony.

Norms of negative consequences might be practiced in a society for a long time. These norms are mostly related to strong beliefs that prevent individuals from violating or abandoning them. In this case, these norms must be removed to reach a stable and benevolent society. Negative norms removal is presented in social science as a part of society evolution, yet it is not modeled in normative multi-agent systems. Norm removal in social science is done in two main stages. The first stage is called collective belief change. The second stage is called collective action. In this paper, we model these two stages into five processes which are, norm negativity realization, collective belief change, norm removal decision, choosing removal monitoring authority, and removal process. When the five stages are completed, agents make their own decision either to delete or not to delete the norm from their cognitive structure depending on their internal system status.

The most common methods for combining different phylogenetic trees with uneven but overlapping taxon sampling are the Matrix Representation with Parsimony (MRP) and consensus tree methods. Although straightforward, some steps of MRP are time-consuming and risky when manually performed, especially the preparation of the matrix representations from the original topologies, and the creation of the single matrix containing all the information of the individual trees. Here we present Building MRP-Matrices (BuM), a free online tool for generating a combined matrix, following Baum and Ragan coding scheme, from files containing phylogenetic trees in parenthetical format.

Summary iTUPA is a free online application for automatizing the Topographic-Unit Parsimony Analysis (TUPA), which identifies areas of endemism based on topography. iTUPA generates species-occurrences matrices based on user-defined topographic units (TUs) and provides a parsimony analysis of the generated matrix. We tested iTUPA after a proposal of regionalization for the Brazilian Atlantic Forest. iTUPA can handle millions of species registers simultaneously and uses Google Earth high-definition maps to visually explore the endemism data. We believe iTUPA is a useful tool for further discussions on biodiversity conservation. Availability and implementation iTUPA is hosted on Google cloud and freely available at http://nuvem.ufabc.edu.br/itupa. iTUPA is implemented using R (version 3.5.1), with RStudio 1.1.453 used as the implementation IDE, Shiny 1.1.0 web framework, and Google Maps® API version 3.36.

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