A fast algorithm for joint reconstruction of ancestral amino acid sequences.
By Tal Pupko, Itsik Pe, Ron Shamir, Dan-Ovidiu Graur. Molecular biology and evolution, 2000
355 citations recorded by the source corpus.
Subfields: Artificial Intelligence, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/c6c99bf73e63afafbc9272ce8d01c85cd1a1d16b
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Artificial Intelligence
- Ziheng Yang
- Tal Pupko
- Osnat Penn
- Daniel J. Wilson
- Xavier Didelot
- Fraser Iain Lewis
- Sergei L. Kosakovsky Pond
- Richard A. Neher
In Molecular Biology
- Sergei L. Kosakovsky Pond
- Simon D. W. Frost
- Art F. Y. Poon
- Fraser Iain Lewis
- Tal Pupko
- Haim Ashkenazy
- Daniel J. Wilson
- Osnat Penn
Citations in the corpus
- An Evolutionary-Network Model Reveals Stratified Interactions in the V3 Loop of the HIV-1 Envelope (2007, methodology): “Using maximum likelihood, we can infer the ancestral sequences D9 at each branching point, or node, of the tree T as a function of D and M [39,40].”
- ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes (2015, methodology): “The ancestral sequences at internal nodes of the clonal genealogy, and any missing base calls in the observed sequences, are reconstructed by ML using a previously described algo-rithm [50].”
- TreeTime: Maximum-likelihood phylodynamic analysis (2017, background): “Given a tree topology and the branch length, the maximum-likelihood ancestral sequences can be inferred in linear time (Felsenstein, 2004; Pupko et al. 2000).”
- FastML: a web server for probabilistic reconstruction of ancestral sequences (2012, methodology): “While MP reconstruction has a time complexity linear in the number of sequences analyzed, efficient algorithms have also been developed for different types of ML-based reconstructions [reviewed in (8)], with a time complexity that is linear with the number of sequence for most algorithms (9,10) and ”
- PAML 4: phylogenetic analysis by maximum likelihood. (2007, background): “The joint reconstruction assigns a set of character states to all ancestral nodes on the tree and is more appropriate when one counts changes at every site (Pupko et al. 2000).”
- Not so different after all: a comparison of methods for detecting amino acid sites under selection. (2005, background): “We consider all models which form a particular case of the general reversible nucleotide model Methods for Detection of Selection 1209 (Lanave et al. 1984; Tavare´ 1986; Rodriguez et al. 1990), whose instantaneous substitution rate matrix is defined by where p A , p C , p G , and p T denote the obser”
- Phylogenetic Analysis by Maximum Likelihood (PAML) (2002, methodology): “The implementation in paml now is based on the algorithm of Pupko et al .”