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Articles by Robert Lanfear
Robust Phylogenetics
Abstract We present a robust phylogenetic inference method, called the trimmed log-likelihood method, which effectively identifies fast-evolving, saturated, or erroneous sites in both simulated and empirical multiple sequence alignments. This method avoids circularity by dynamically identifying and removing sites without relying on an initial tree, allowing the specific sites removed to change as tree topology and branch lengths are estimated.
Selecting a Window Size for the Analysis of Whole Genome Alignments using AIC
Abstract The variation of evolutionary histories along the genome presents a challenge for phylogenomic methods to identify the non-recombining regions and reconstruct the phylogenetic tree for each region. To address this problem, many studies used the non-overlapping window approach, often with an arbitrary selection of fixed window sizes that potentially include intra-window recombination events.
MixtureFinder: Estimating DNA mixture models for phylogenetic analyses
Abstract In phylogenetic studies, both partitioned models and mixture models are used to account for heterogeneity in molecular evolution among the sites of DNA sequence alignments. Partitioned models require the user to specify the grouping of sites into subsets, and then assume that each subset of sites can be modelled by a single common process.
Testing for Phylogenetic Signal in Single-Cell RNA-Seq Data
Journal of Computational BiologyAhead of Print ICCABS 2021Open AccessCreative Commons license Abstract Phylogenetic methods are emerging as a useful tool to understand cancer evolutionary dynamics, including tumor structure, heterogeneity, and progression. Most currently used approaches utilize either bulk whole genome sequencing or single-cell DNA sequencing and are based on calling copy number alterations and single nucleotide variants (SNVs).
MAST: Phylogenetic Inference with Mixtures Across Sites and Trees
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Updated site concordance factors minimize effects of homoplasy and taxon sampling
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AliSim: A Fast and Versatile Phylogenetic Sequence Simulator For the Genomic Era
Abstract Sequence simulators play an important role in phylogenetics. Simulated data has many applications, such as evaluating the performance of different methods, hypothesis testing with parametric bootstraps, and, more recently, generating data for training machine-learning applications. Many sequence simulation programs exist, but the most feature-rich programs tend to be rather slow, and the fastest programs tend to be feature-poor.
Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression
Loading metrics Open Access Peer-reviewed Research Article Dan Vanderpool , Bui Quang Minh, Robert Lanfear, Daniel Hughes, Shwetha Murali, R. Alan Harris, Muthuswamy Raveendran, Donna M. Muzny, Mark S. Hibbins, Robert J. Williamson, Richard A. Gibbs, Kim C. Worley, Jeffrey Rogers, Matthew W. Hahn Dan Vanderpool, Bui Quang Minh, Robert Lanfear, Daniel Hughes, Shwetha Murali, R. Alan Harris, Muthuswamy Raveendran, Donna M. Muzny, Mark S. Hibbins, Robert J.
Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Non-Reversible Models
Abstract Using time-reversible Markov models is a very common practice in phylogenetic analysis, because although we expect many of their assumptions to be violated by empirical data, they provide high computational efficiency. However, these models lack the ability to infer the root placement of the estimated phylogeny.
QMaker: Fast and accurate method to estimate empirical models of protein evolution
New Results View ORCID ProfileBui Quang Minh, Cuong Cao Dang, Le Sy Vinh, Robert Lanfear doi: https://doi.org/10.1101/2020.02.20.958819 Abstract Amino acid substitution models play a crucial role in phylogenetic analyses. Maximum likelihood (ML) methods have been proposed to estimate amino acid substitution models, however, they are typically complicated and slow.
Troubleshooting Public Data Archiving: Suggestions to Increase Participation
Loading metrics Open Access Perspective Dominique G. Roche , Robert Lanfear, Sandra A. Binning, Tonya M. Haff, Lisa E. Schwanz, Kristal E. Cain, Hanna Kokko, Michael D. Jennions, Loeske E. B. Kruuk Dominique G. Roche, Robert Lanfear, Sandra A. Binning, Tonya M. Haff, Lisa E. Schwanz, Kristal E. Cain, Hanna Kokko, Michael D. Jennions, Loeske E. B.
Do plants have a segregated germline?
Copyright: © 2018 Robert Lanfear. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: Australian Research Council (grant number FT140100843). Future Fellowship to R. Lanfear. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Public Data Archiving in Ecology and Evolution: How Well Are We Doing?
Loading metrics Open Access Perspective Dominique G. Roche , Loeske E. B. Kruuk, Robert Lanfear, Sandra A. Binning Dominique G. Roche, Loeske E. B. Kruuk, Robert Lanfear, Sandra A. Binning Published: November 10, 2015 https://doi.org/10.1371/journal.pbio.1002295 Figures Abstract Policies that mandate public data archiving (PDA) successfully increase accessibility to data underlying scientific publications. However, is the data quality sufficient to allow reuse and reanalysis?
Evidence of Experimental Bias in the Life Sciences: Why We Need Blind Data Recording
Loading metrics Open Access Perspective Luke Holman , Megan L. Head , Robert Lanfear, Michael D. Jennions Luke Holman, Megan L. Head, Robert Lanfear, Michael D. Jennions Published: July 8, 2015 https://doi.org/10.1371/journal.pbio.1002190 Figures Abstract Observer bias and other “experimenter effects” occur when researchers’ expectations influence study outcome.
The American Naturalist, Ahead of Print, p. 000
A new view is emerging of the interplay between mutation at the genomic level, substitution at the population level, and diversification at the lineage level. Many studies have suggested that rate of molecular evolution is linked to rate of diversification, but few have evaluated competing hypotheses.
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