Results 241 to 250 of about 13,467,690 (274)

A Consensus Method for Ancestral Recombination Graphs

Journal of Molecular Evolution, 2017
We propose a consensus method for ancestral recombination graphs (ARGs) that generates a single ARG representing commonalities among a cloud of ARGs defined for the same genomic region and set of taxa. Our method, which we call "threshold consensus," treats a genomic location as a potential recombination breakpoint only if the number of ARGs in the ...
Mary K. Kuhner, Jon Yamato
openaire   +2 more sources

SBEARS—A Site-Based Method to Estimate Ancestral Ranges of Species

Evolution; International Journal of Organic Evolution
Abstract Assessing the geographic dimension of diversification is paramount to integrate macroecology and macroevolution. Estimating ancestral ranges of species from phylogenies and spatial distribution of extant species has been fundamental for historical biogeography and can help in this endeavor.
Renan Maestri, Gabriel Nakamura, Fabricio Villalobos   +2 more
exaly   +3 more sources

Assessing Ancestral Genome Reconstruction Methods by Resampling

2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2014
Inference of ancestral or extinct genomes is important in evolutionary biology, cancer research and many other research areas. Whole-genome data has become readily available due to advances in large-scale sequencing technology. During the past decades, a number of evolutionary models and related algorithms have been designed to infer ancestral genome ...
Jijun Tang, William Hoskins
exaly   +2 more sources

Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods II

Journal of Computational Biology, 2010
Since the availability of assembled eukaryotic genomes, the first one being a budding yeast, many computational methods for the reconstruction of ancestral karyotypes and gene orders have been developed. The difficulty has always been to assess their reliability, since we often miss a good knowledge of the true ancestral genomes to compare their ...
Chauve, Cedric, Gavranovic, Haris, Ouangraoua, Aida, Tannier, Eric   +3 more
openaire   +4 more sources

Accuracies of Ancestral Amino Acid Sequences Inferred by the Parsimony, Likelihood, and Distance Methods [PDF]

Journal of Molecular Evolution, 1997
Information about protein sequences of ancestral organisms is important for identifying critical amino acid substitutions that have caused the functional change of proteins in evolution. Using computer simulation, we studied the accuracy of ancestral amino acids inferred by two currently available methods (maximum-parsimony [MP] and maximum-likelihood [
Jianzhi Zhang, Masatoshi Nei
exaly   +3 more sources

Using Ancestral State Reconstruction Methods for Onomasiological Reconstruction in Multilingual Word Lists [PDF]

Language Dynamics and Change, 2018
AbstractCurrent efforts in computational historical linguistics are predominantly concerned with phylogenetic inference. Methods for ancestral state reconstruction have only been applied sporadically. In contrast to phylogenetic algorithms, automatic reconstruction methods presuppose phylogenetic information in order to explain what has evolved when ...
Gerhard Jäger, Johann-Mattis List
exaly   +5 more sources

Tracing Ancestral Specificity of Lectins: Ancestral Sequence Reconstruction Method as a New Approach in Protein Engineering

2014
Protein evolution is a process of molecular design leading to the diversity of functional proteins found in nature. Recent advances in bioinformatics and structural biology, in addition to recombinant protein expression techniques, enable us to analyze more directly the molecular evolution of proteins by a new method using ancestral sequence ...
Tomohisa, Ogawa, Tsuyoshi, Shirai
openaire   +2 more sources

Analyzing the Fitch Method for Reconstructing Ancestral States on Ultrametric Phylogenetic Trees

Bulletin of Mathematical Biology, 2010
The accuracy of the Fitch method for reconstructing ancestral states on ultrametric phylogenetic trees is studied. Two recurrence relations for computing the accuracy are given here. Using these relations, we analyze the convergence of the accuracy of the Fitch method for reconstructing the root state on a complete binary tree of 2( n ) leaves as n ...
Zhang, L., Shen, J., Yang, J., Li, G.
openaire   +3 more sources

Evaluation of Ancestral Sequence Reconstruction Methods to Infer Nonstationary Patterns of Nucleotide Substitution [PDF]

Genetics, 2015
AbstractInference of gene sequences in ancestral species has been widely used to test hypotheses concerning the process of molecular sequence evolution. However, the approach may produce spurious results, mainly because using the single best reconstruction while ignoring the suboptimal ones creates systematic biases.
Hiroshi Akashi, Tomotaka Matsumoto, Ziheng Yang   +2 more
exaly   +3 more sources

Efficient estimation of the accuracy of the maximum likelihood method for ancestral state reconstruction

Journal of Combinatorial Optimization, 2009
zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Ma, B., Zhang, L.
openaire   +2 more sources