iTUPA: an online automated application to perform Topographic-Unit Parsimony Analysis

Muhsen Hammoud; Charles Morphy D Santos; João Paulo Gois

doi:10.1093/bioinformatics/btz487

iTUPA: an online automated application to perform Topographic-Unit Parsimony Analysis

Bioinformatics. 2019 Nov 1;35(22):4818-4820. doi: 10.1093/bioinformatics/btz487.

Authors

Muhsen Hammoud¹, Charles Morphy D Santos², João Paulo Gois¹

Affiliations

¹ Center for Mathematics, Computing, and Cognition, Santo André, São Paulo, Brazil.
² Center for Natural and Human Sciences, Federal University of ABC, Santo André, São Paulo, Brazil.

PMID: 31197309
DOI: 10.1093/bioinformatics/btz487

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Biodiversity*
Software*