Results 51 to 60 of about 850,464 (362)

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

Systematic Biology, 2012
Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest
F. Ronquist, M. Teslenko, Paul van der Mark, Daniel L. Ayres, A. Darling, S. Höhna, B. Larget, Liang Liu, M. Suchard, J. Huelsenbeck   +9 more
semanticscholar   +1 more source

Polyploid phylogenetics [PDF]

New Phytologist, 2021
SummaryPolyploidy is a dominant feature of extant plant diversity. However, major research questions, including whether polyploidy is important to long‐term evolution or is just ‘evolutionary noise’, remain unresolved due to difficulties associated with the generation and analysis of data from polyploid lineages.
openaire   +2 more sources

Description of the Three Complete Mitochondrial Genomes of Click Beetles (Coleoptera, Elateridae) with Phylogenetic Implications

Taxonomy, 2023
The family Elateridae, known as click beetles, is a mega-diverse lineage of Coleoptera. Wireworms are the larval stage of click beetles, which are generalist herbivores and which are recognized as economically important pests of crops.
Nan Song, Xingyu Lin, Te Zhao
doaj   +1 more source

W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis

Nucleic Acids Res., 2016
This article presents W-IQ-TREE, an intuitive and user-friendly web interface and server for IQ-TREE, an efficient phylogenetic software for maximum likelihood analysis.
Jana Trifinopoulos, Lam-Tung Nguyen, A. Haeseler, B. Minh   +3 more
semanticscholar   +1 more source

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

bioRxiv, 2018
Motivation Phylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture, and medicine.
Alexey M. Kozlov, D. Darriba, T. Flouri, Benoit Morel, A. Stamatakis   +4 more
semanticscholar   +1 more source

A Format for Phylogenetic Placements [PDF]

PLoS ONE, 2012
We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g. short reads) into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and post-processing phylogenetic placements, and the lack of an established standard for storing them.
Frederick A. Matsen, Alexandros Stamatakis, Aaron Gallagher, Noah G. Hoffman, Noah G. Hoffman   +4 more
openaire   +6 more sources

Caracterização molecular do vírus da raiva isolado de Desmodus rotundus capturados no Estado do Rio de Janeiro Molecular characterization of rabies virus isolated from Desmodus rotundus captured in Rio de Janeiro State

Arquivo Brasileiro de Medicina Veterinária e Zootecnia, 2010
Caracterizou-se filogeneticamente o vírus da raiva, isolado de morcegos hematógafos (Demodus rotundus). Cento e noventa e nove D. rotundus foram capturados em cinco abrigos, no Norte e Noroeste do Estado do Rio de Janeiro e sul do Espírito Santo.
L.F.P. Vieira, S.R.F.G. Pereira, P.E. Brandão, R.N. Oliveira, P. Carnieli-Junior, A.C. Galante, C.N. Chicarino, I. Kotait   +7 more
doaj   +1 more source

PAML 4: phylogenetic analysis by maximum likelihood.

Molecular biology and evolution, 2007
PAML, currently in version 4, is a package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). The programs may be used to compare and test phylogenetic trees, but their main strengths lie in the rich ...
Ziheng Yang
semanticscholar   +1 more source

Improved Understanding of the Macrofungal Diversity of Mongolia: Species Richness, Conservation Status, and An Annotated Checklist

Mycobiology
In this study, we updated and revised the checklist of macrofungi, along with the distribution of phytogeographical regions and the regional conservation status in Mongolia.
Nyamsuren Kherlenchimeg, Ganbaatar Burenbaatar, Shukherdorj Baasanmunkh, Zagarjav Tsegmed, Magsar Urgamal, Tolgor Bau, Sang-Kuk Han, Seung-Yoon Oh, Hyeok Jae Choi   +8 more
doaj   +1 more source

ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data

, 2017
We present an r package, ggtree, which provides programmable visualization and annotation of phylogenetic trees. ggtree can read more tree file formats than other softwares, including newick, nexus, NHX, phylip and jplace formats, and support ...
Guangchuang Yu, David K. Smith, Huachen Zhu, Y. Guan, T. Lam   +4 more
semanticscholar   +1 more source