Biology subjects

Sanchez Reyes, L. L.

Publications and source records attributed to Sanchez Reyes, L. L..

3 recordsLinked to original sources

bioRxiv2020

OpenTree: A Python package for Accessing andAnalyzing data from the Open Tree of Life

The Open Tree of Life project constructs a comprehensive, dynamic and digitally-available tree of life by synthesizing published phylogenetic trees along with taxonomic data. Open Tree of Life provides web-service application programming interfaces (APIs) to make the tree estimate, unified taxonomy, and input phylogenetic data available to anyone. Here, we describe the python package opentree, which provides a user friendly python wrapper for these APIs and a set of scripts and tutorials for straightforward downstream data analyses. We demonstrate the utility of these tools by generating an estimate of the phylogenetic relationships of all bird families, and by capturing a phylogenetic estimate for all taxa observed at the University of California Merced Vernal Pools and Grassland Reserve.

bioinformatics↗

bioRxiv2020

Physcraper: A Python package for continual update of evolutionary estimates using the Open Tree of Life

O_LIPhylogenies are a key part of research in many areas of biology. Tools that automate some parts of the process of phylogenetic reconstruction, mainly molecular character matrix assembly, have been developed for the advantage of both specialists in the field of phylogenetics and nonspecialists. However, interpretation of results, comparison with previously available phylogenetic hypotheses, and selection of one phylogeny for downstream analyses and discussion still impose difficulties to one that is not a specialist either on phylogenetic methods or on a particular group of study. C_LIO_LIPhyscraper is a command-line Python program that automates the update of published phylogenies by adding public DNA sequences to underlying alignments of previously published phylogenies. It also provides a framework for straightforward comparison of published phylogenies with their updated versions, by leveraging upon tools from the Open Tree of Life project to link taxonomic information across databases. C_LIO_LIPhyscraper can be used by the nonspecialist, as a tool to generate phylogenetic hypotheses based on publicly available expert phylogenetic knowledge. Phylogeneticists and taxonomic group specialists will find it useful as a tool to facilitate molecular dataset gathering and comparison of alternative phylogenetic hypotheses (topologies). C_LIO_LIThe Physcraper workflow demonstrates the benefits of doing open science for phylogenetics, encour-aging researchers to strive for better sharing practices. Physcraper can be used with any OS and is released under an open-source license. Detailed instructions for installation and use are available at https://physcraper.readthedocs. C_LI

bioinformatics↗

bioRxiv2019

Datelife: leveraging databases and analytical tools to reveal the dated Tree of Life.

Achieving a high-quality reconstruction of a phylogenetic tree with branch lengths proportional to absolute time (chronogram) is a difficult and time-consuming task. But the increased availability of fossil and molecular data, and time-efficient analytical techniques has resulted in many recent publications of large chronograms for a large number and wide diversity of organisms. Knowledge of the evolutionary time frame of organisms is key for research in the natural sciences. It also represent valuable information for education, science communication, and policy decisions. When chronograms are shared in public and open databases, this wealth of expertly-curated and peer-reviewed data on evolutionary timeframe is exposed in a programatic and reusable way, as intensive and localized efforts have improved data sharing practices, as well as incentivizited open science in biology. Here we present DateLife, a service implemented as an R package and an R Shiny website application available at www.datelife.org, that provides functionalities for efficient and easy finding, summary, reuse, and reanalysis of expert, peer-reviewed, public data on time frame of evolution. The main DateLife workflow constructs a chronogram for any given combination of taxon names by searching a local chronogram database constructed and curated from the Open Tree of Life Phylesystem phylogenetic database, which incorporates phylogenetic data from the TreeBASE database as well. We implement and test methods for summarizing time data from multiple source chronograms using supertree and congruification algorithms, and using age data extracted from source chronograms as secondary calibration points to add branch lengths proportional to absolute time to a tree topology. DateLife will be useful to increase awareness of the existing variation in alternative hypothesis of evolutionary time for the same organisms, and can foster exploration of the effect of alternative evolutionary timing hypotheses on the results of downstream analyses, providing a framework for a more informed interpretation of evolutionary results.

scientific communication and education↗