منابع مشابه
The Phylogenetic Likelihood Library
We introduce the Phylogenetic Likelihood Library (PLL), a highly optimized application programming interface for developing likelihood-based phylogenetic inference and postanalysis software. The PLL implements appropriate data structures and functions that allow users to quickly implement common, error-prone, and labor-intensive tasks, such as likelihood calculations, model parameter as well as...
متن کاملMaximum likelihood of phylogenetic networks
MOTIVATION Horizontal gene transfer (HGT) is believed to be ubiquitous among bacteria, and plays a major role in their genome diversification as well as their ability to develop resistance to antibiotics. In light of its evolutionary significance and implications for human health, developing accurate and efficient methods for detecting and reconstructing HGT is imperative. RESULTS In this art...
متن کاملPenalized likelihood phylogenetic inference: bridging the parsimony-likelihood gap.
The increasing diversity and heterogeneity of molecular data for phylogeny estimation has led to development of complex models and model-based estimators. Here, we propose a penalized likelihood (PL) framework in which the levels of complexity in the underlying model can be smoothly controlled. We demonstrate the PL framework for a four-taxon tree case and investigate its properties. The PL fra...
متن کاملAn Investigation of Phylogenetic Likelihood Methods
We analyze the performance of likelihoodbased approaches used to reconstruct phylogenetic trees. Unlike other techniques such as Neighbor-Joining (NJ) and Maximum Parsimony (MP), relatively little is known regarding the behavior of algorithms founded on the principle of likelihood. We study the accuracy, speed, and likelihood scores of four representative likelihood-based methods (fastDNAml, Mr...
متن کاملPhylogenetic estimation with partial likelihood tensors
We present an alternative method for calculating likelihoods in molecular phylogenetics. Our method is based on partial likelihood tensors, which are generalizations of partial likelihood vectors, as used in Felsenstein's approach. Exploiting a lexicographic sorting and partial likelihood tensors, it is possible to obtain significant computational savings. We show this on a range of simulated d...
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ژورنال
عنوان ژورنال: Journal of Molecular Evolution
سال: 2021
ISSN: 0022-2844,1432-1432
DOI: 10.1007/s00239-020-09982-w