Software

Salphycon is a shiny app that extends the functionalities of the (phruta) R package. Salphycon is able to (1) find potentially (phylogenetically) relevant gene regions for a given set of taxa on GenBank, (2) retrieve gene sequences and curate taxonomic information from the same database, (3) combine downloaded and local gene sequences, and (4) perform sequence alignment, phylogenetic inference, and basic tree dating tasks. Both phruta and salphycon are focused on species-level analyses.

Barrio Map offers fundamental functionalities like finding locations by conducting searches or selecting coordinates. Users can select from predefined scales and export the scaled maps to particular page sizes. Maps generated using Barrio Map are formal descriptions of particular sites with defined values of resolution, scales, and explicit information on distances. Barrio Map, in conjunction with OpenStreetMaps, is written in R, with functionalities largely leveraged from packages such as Leaflet and Shiny.

CityComp is a Shiny app developed to support the use of the comparative framework developed in Arechiga et al. (2023). In the app, users can directly visualize the results presented in the same paper. Specifically, a graphical and interactive version of Fig. 6 in the same paper is presented in the app. Users can further define a target city and estimate their similarity to cities across the globe. Dynamic filtering and mapping are implemented within the app.

This tool predicts Escherichia coli (E. coli) levels in the Upper Santa Cruz River using a model trained on public data from 2009-2022. It is intended as a warning of possible high bacterial loads; water quality must still be verified using coliform testing procedures to ensure public safety.

The phruta R package is designed to simplify the basic phylogenetic pipeline. All the code is run within the same program and data from intermediate steps are saved in independent folders (optional). phruta retrieves gene sequences, combines newly downloaded to local gene sequences, performs sequence alignments, and basic phylogenetic inference.

The data.table package enables high-performance extended functionality for data tables in R. treedata.table is a wrapper for data.table for phylogenetic analyses that matches a phylogeny to the data.table, and preserves matching during data.table operations.

Bayesian Additive Regression Networks. We apply Bayesian Additive Regression Tree (BART) principles to training an ensemble of small neural networks for regression tasks. Using Markov Chain Monte Carlo, Bayesian Additive Regression Net- works (BARN) samples from the space of single hidden layer neural networks that are conditioned on their fit to data. You can find more information in barnpy and its associated documentation