Estimating a binary character's effect on speciation and extinction.
This work describes how to calculate the probability that a group of extant species would have evolved as observed, given a particular model of the character's effect, under a simple model of evolution (the "BiSSE model, binary-state speciation and extinction).
The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
The BioCyc PGDBs generated by SRI are offered for adoption by any interested party for the ongoing integration of metabolic and genome-related information about an organism.
An Introduction to Phylogenetically Based Statistical Methods, with a New Method for Confidence Intervals on Ancestral Values
Three phylogenetically based statistical methods are presented, including phylogenetically independent contrasts, Monte Carlo computer simulations to obtain null distributions of test statistics, and phylogenetic autocorrelation, which allow traditional topics in comparative and ecological physiology to be addressed with greater rigor.
Synthesis of phylogeny and taxonomy into a comprehensive tree of life
- Cody E. Hinchliff, Stephen A. Smith, K. Cranston
- Biology, Environmental ScienceProceedings of the National Academy of Sciences
- 8 December 2014
This study is the first, to the knowledge, to apply an efficient and automated process for assembling published trees into a complete tree of life, and presents a draft tree containing 2.3 million tips—the Open Tree of Life.
The MetaCyc database of metabolic pathways and enzymes
This article provides an update on the developments in MetaCyc during the past two years, including the expansion of data and addition of new features.
The MetaCyc database of metabolic pathways and enzymes - a 2019 update
This article provides an update on the developments in MetaCyc during September 2017 to August 2019, up to version 23.1.1, which includes modifications to the GlycanBuilder software that enable displaying glycans using symbolic representation, improved graphics and fonts for web displays, and improvements in the PathoLogic component of Pathway Tools.
Within-species variation and measurement error in phylogenetic comparative methods.
Most phylogenetically based statistical methods for the analysis of quantitative or continuously varying phenotypic traits assume that variation within species is absent or at least negligible, which…
Exploring power and parameter estimation of the BiSSE method for analyzing species diversification
It is found that the power of the BiSSE method is severely affected by both sample size and high tip ratio bias, and future studies utilizing BiS SE that have fewer than 300 terminals and/or have datasets where highTip ratio bias is observed should be extremely cautious with the interpretation of hypothesis testing results.
The BioCyc collection of microbial genomes and metabolic pathways
BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical…
NeXML: Rich, Extensible, and Verifiable Representation of Comparative Data and Metadata
This paper describes how the use of NeXML by the TreeBASE and Phenoscape projects satisfies user needs that cannot be satisfied with other available file formats, and proposes an XML standard that supports exchange of richly annotated comparative data that is both flexible and rigorous.