Results 31 to 40 of about 35,511 (272)

Phycas: Software for Bayesian Phylogenetic Analysis [PDF]

Systematic Biology, 2015
Phycas is open source, freely available Bayesian phylogenetics software written primarily in C++ but with a Python interface. Phycas specializes in Bayesian model selection for nucleotide sequence data, particularly the estimation of marginal likelihoods, central to computing Bayes Factors.
Paul O, Lewis, Mark T, Holder, David L, Swofford   +2 more
openaire   +2 more sources

The Effect of Sample Bias and Experimental Artefacts on the Statistical Phylogenetic Analysis of Picornaviruses

Viruses, 2019
Statistical phylogenetic methods are a powerful tool for inferring the evolutionary history of viruses through time and space. The selection of mathematical models and analysis parameters has a major impact on the outcome, and has been relatively well ...
Yulia Vakulenko, Andrei Deviatkin, Alexander Lukashev   +2 more
doaj   +1 more source

A topology-marginal composite likelihood via a generalized phylogenetic pruning algorithm

Algorithms for Molecular Biology, 2023
Bayesian phylogenetics is a computationally challenging inferential problem. Classical methods are based on random-walk Markov chain Monte Carlo (MCMC), where random proposals are made on the tree parameter and the continuous parameters simultaneously ...
Seong-Hwan Jun, Hassan Nasif, Chris Jennings-Shaffer, David H Rich, Anna Kooperberg, Mathieu Fourment, Cheng Zhang, Marc A Suchard, Frederick A Matsen   +8 more
doaj   +1 more source

Testing use of mitochondrial COI sequences for the identification and phylogenetic analysis of New Zealand caddisflies (Trichoptera) [PDF]

, 2009
We tested the hypothesis that cytochrome c oxidase subunit 1 (COI) sequences would successfully discriminate recognised species of New Zealand caddisflies. We further examined whether phylogenetic analyses, based on the COI locus, could recover currently
Banks, Jonathan C., DeWaard, Jeremy R., Hebert, Paul D.N., Hogg, Ian D., Smith, Brian J.   +4 more
core   +2 more sources

Rapid evolution and biogeographic spread in a colorectal cancer

Nature Communications, 2019
The clonal origins of metastases and the timing of dissemination remains an open question for most cancer types. Using primary and metastatic samples taken from one colorectal cancer patient, Alves et al.
Joao M. Alves, Sonia Prado-López, José Manuel Cameselle-Teijeiro, David Posada   +3 more
doaj   +1 more source

Robust Phylodynamic Analysis of Genetic Sequencing Data from Structured Populations

Viruses, 2022
The multi-type birth–death model with sampling is a phylodynamic model which enables the quantification of past population dynamics in structured populations based on phylogenetic trees.
Jérémie Scire, Joëlle Barido-Sottani, Denise Kühnert, Timothy G. Vaughan, Tanja Stadler   +4 more
doaj   +1 more source

Into the Light: Diurnality has Evolved Multiple Times in Geckos [PDF]

, 2015
Geckos are the only major lizard group consisting mostly of nocturnal species. Nocturnality is presumed to have evolved early in gecko evolution and geckos possess numerous adaptations to functioning in low light and at low temperatures. However, not all
Bauer, Aaron M., Gamble, Tony, Greenbaum, E., Jackman, Todd R.   +3 more
core   +2 more sources

Posterior Predictive Bayesian Phylogenetic Model Selection [PDF]

Systematic Biology, 2013
We present two distinctly different posterior predictive approaches to Bayesian phylogenetic model selection and illustrate these methods using examples from green algal protein-coding cpDNA sequences and flowering plant rDNA sequences. The Gelfand-Ghosh (GG) approach allows dissection of an overall measure of model fit into components due to posterior
Paul O, Lewis, Wangang, Xie, Ming-Hui, Chen, Yu, Fan, Lynn, Kuo   +4 more
openaire   +2 more sources

Wandering behaviour prevents inter and intra oceanic speciation in a coastal pelagic fish [PDF]

, 2017
Small pelagic fishes have the ability to disperse over long distances and may present complex evolutionary histories. Here, Old World Anchovies (OWA) were used as a model system to understand genetic patterns and connectivity of fish between the Atlantic
A Magoulas, A Moan Le, AGF Teacher, AGK Mirams, BW Bowen, CP Burridge, D Duchene, D Posada, DM Sigman, G Silva, H Akaike, HA Lessios, HA Lessios, I Montes, I Zarraonaindia, J DiBattista, JB Horne, JB Kristoffersen, JC Briggs, JC Briggs, JR Marlow, JS Reece, JX Liu, K Keenan, K Tamura, L Cárdenas, L Excoffier, L Jost, LA Rocha, N Ryman, N Sanz, P Beerli, P Beerli, P Beerli, P Borsa, PG Meirmans, PS Pennings, PW Hedrick, R Bouckaert, R Henriques, R Jansson, RA Schwartzlose, S Guindon, S Jemaa, S Lavoué, SR Palumbi, T Gernhard, T Jombart, WS Grant, WS Grant, WS Grant, WS Grant   +51 more
core   +2 more sources

Bayesian Phylogenetic Analysis of Combined Data [PDF]

Systematic Biology, 2004
The recent development of Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) techniques has facilitated the exploration of parameter-rich evolutionary models. At the same time, stochastic models have become more realistic (and complex) and have been extended to new types of data, such as morphology.
Johan A A, Nylander, Fredrik, Ronquist, John P, Huelsenbeck, José Luis, Nieves-Aldrey   +3 more
openaire   +3 more sources