Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees
By Kevin J. Liu, Sindhu Raghavan, Serita M. Nelesen, C. Linder, Tandy J. Warnow. Science, 2009
498 citations recorded by the source corpus.
Subfields: Genetics, Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/21d19bd857a4008777de4c60014b33621812ae4c
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Genetics
- Kazutaka Katoh
- Siavash Mirarab
- Tal Pupko
- Haim Ashkenazy
- Manuel Gil
- Tandy J. Warnow
- Daniela Börnigen
- Curtis Huttenhower
In Molecular Biology
- Kazutaka Katoh
- Curtis Huttenhower
- Nicola Segata
- Siavash Mirarab
- Haim Ashkenazy
- Xochitl C. Morgan
- Tal Pupko
- Christophe Dessimoz
In Plant Science
- Manuel Gil
- Tandy J. Warnow
- Tal Pupko
- Siavash Mirarab
- Haim Ashkenazy
- Kazutaka Katoh
- Christophe Dessimoz
Citations in the corpus
- PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes (2013, methodology): “Different tree reconstruction algorithms can be used with the selected residues, and this raises the possibility of evaluating additional evolutional models and tree-combining 55 or alignment-free 56 reconstructions.”
- American Gut: an Open Platform for Citizen Science Microbiome Research (2018, unknown): “SEPP uses the simultaneous alignment and tree estimation strategy described in reference 53 to identify reasonable placements for sequence fragments within an existing phylogeny and alignment.”
- GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters (2015, methodology): “Within the maximum-likelihood framework, this is feasible using programs such as SATe (47,48).”
- Phylogenetic Systematics of Dart-Poison Frogs and Their Relatives Revisited (Anura: Dendrobatoidea) (2017, methodology): “That difference means that, unlike MALIGN, SATé’s optimal solution is necessarily a trivial alignment, with selection of a nontrivial alignment owing to inadequate iterative searching (Denton and Wheeler, 2012).”
- Global diversity and distribution of arbuscular mycorrhizal fungi (2011, unknown): “We also used SATé to estimate phylogenies using the default parameters of 100 iterations under the Gamma GTR substitution model (Figs.”
- PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences (2015, methodology): “Nucleotide: To explore performance on moderate-sized datasets, we used the 1000-sequence nucleotide datasets with average length 1000–1023 from Liu et al. (2009), which were generated using ROSE (Stoye et al., 1998).”