PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories.

PubWeight™: 0.75‹?›

🔗 View Article (PMID 27472806)

Published in PLoS Comput Biol on July 29, 2016

Authors

Victor Hanson-Smith1, Alexander Johnson1

Author Affiliations

1: Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America.

Articles citing this

Resurrecting ancestral genes in bacteria to interpret ancient biosignatures. Philos Trans A Math Phys Eng Sci (2017) 0.75

Articles cited by this

MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol (2010) 53.37

PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol (2007) 45.68

FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One (2010) 26.15

Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol (1994) 24.04

RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics (2004) 20.94

ProtTest: selection of best-fit models of protein evolution. Bioinformatics (2005) 19.16

Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst Biol (2006) 12.96

A new method of inference of ancestral nucleotide and amino acid sequences. Genetics (1995) 10.23

A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol (2004) 7.34

DendroPy: a Python library for phylogenetic computing. Bioinformatics (2010) 5.09

Alignment uncertainty and genomic analysis. Science (2008) 4.09

Crystal structure of an ancient protein: evolution by conformational epistasis. Science (2007) 3.56

Multiple sequence alignment. Curr Opin Struct Biol (2006) 2.93

Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol (2011) 2.66

MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities. Bioinformatics (2010) 2.53

Resurrecting ancient genes: experimental analysis of extinct molecules. Nat Rev Genet (2004) 2.38

Evolutionary biochemistry: revealing the historical and physical causes of protein properties. Nat Rev Genet (2013) 1.76

Analyzing protein structure and function using ancestral gene reconstruction. Curr Opin Struct Biol (2010) 1.68

Assessing the accuracy of ancestral protein reconstruction methods. PLoS Comput Biol (2006) 1.62

Evolution of increased complexity in a molecular machine. Nature (2012) 1.58

Accounting for alignment uncertainty in phylogenomics. PLoS One (2012) 1.35

Robustness of ancestral sequence reconstruction to phylogenetic uncertainty. Mol Biol Evol (2010) 1.20

Evolutionary history and metabolic insights of ancient mammalian uricases. Proc Natl Acad Sci U S A (2014) 1.18

Evolution of a new function by degenerative mutation in cephalochordate steroid receptors. PLoS Genet (2008) 1.14

Following gene duplication, paralog interference constrains transcriptional circuit evolution. Science (2013) 1.10

Evolution of DNA specificity in a transcription factor family produced a new gene regulatory module. Cell (2014) 0.92

Ancestral resurrection reveals evolutionary mechanisms of kinase plasticity. Elife (2014) 0.83