RESUMO
Current frameworks of side-by-side phylogenetic trees comparison face two issues: (1) accepting mainly binary trees as input and (2) assuming input trees having identical or highly overlapping taxa. However, cladistic comparative studies often lead with multiple nontotally resolved trees with nonidentical sets of taxa. We tackle these issues in this study, presenting the iPhyloC, an interactive web-based framework for comparing phylogenetic trees side by side. iPhyloC supports automatic identification of the common taxa in the input trees, comparison options between them, intuitive design, high usability, scalability to large trees, and cross-platform support. iPhyloC was tested using different trees and a supertree depicting the phylogenetic relationships within the insect order Diptera as examples.
Assuntos
Algoritmos , Biologia Computacional , Internet , FilogeniaRESUMO
Seeded segmentation methods have gained a lot of attention due to their good performance in fragmenting complex images, easy usability and synergism with graph-based representations. These methods usually rely on sophisticated computational tools whose performance strongly depends on how good the training data reflect a sought image pattern. Moreover, poor adherence to the image contours, lack of unique solution, and high computational cost are other common issues present in most seeded segmentation methods. In this work we introduce Laplacian Coordinates, a quadratic energy minimization framework that tackles the issues above in an effective and mathematically sound manner. The proposed formulation builds upon graph Laplacian operators, quadratic energy functions, and fast minimization schemes to produce highly accurate segmentations. Moreover, the presented energy functions are not prone to local minima, i.e., the solution is guaranteed to be globally optimal, a trait not present in most image segmentation methods. Another key property is that the minimization procedure leads to a constrained sparse linear system of equations, enabling the segmentation of high-resolution images at interactive rates. The effectiveness of Laplacian Coordinates is attested by a comprehensive set of comparisons involving nine state-of-the-art methods and several benchmarks extensively used in the image segmentation literature.
RESUMO
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.
Assuntos
Filogenia , Animais , InternetRESUMO
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.
