SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.

By Kevin J. Liu, Tandy J. Warnow, Mark T. Holder, Serita M. Nelesen, Jiaye Yu, Alexandros Stamatakis, And C Randal Linder, Liu K, R. S, Nelesen S Linder. Systematic Biology, 2012

353 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/101bebfd49cb2cab2dfdc1828db8d1eabd92b2c0

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Citations in the corpus

Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics (2014, methodology): “With the recent advance in large-scale alignment and tree inference tools (Liu et al. 2012; Stamatakis et al. 2012; Katoh and Standley 2013), it is the time to fully take advantage of the information in gene trees to obtain more complete and more accurate homolog and ortholog sets.”
Functional and phylogenetic assembly in a Chinese tropical tree community across size classes, spatial scales and habitats (2014, methodology): “The trnH-psbA and ITS regions were aligned within families using software package SAT e (Liu et al. 2012a) and then concatenated to the rbcL and matK alignments.”
Pitfalls in supermatrix phylogenomics (2017, neutral): “In contrast, it is unclear whether it is better to continue improving the current strategies based on a “static” supermatrix, or to further develop methods that simultaneously perform alignment and phylogenetic inference of a supermatrix (Hein 1990; Liu et al. 2012) or to develop methods that simult”
Phylotranscriptomic analysis of the origin and early diversification of land plants (2014, methodology): “Simultaneous alignment and tree estimation (SATé) (57) alignments of the 852 orthogroups were used to estimate phylogenetic relationships through supermatrix, supertree, and coalescent-based species tree approaches.”
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).”
Standard methods for molecular research in Apis mellifera (2013, methodology): “An alternative software package to MEGA for ML analyses is SATé (Simultaneous Alignment and Tree estimation; Liu et al., 2012), which infers sequence alignment and tree building concurrently as an iterative process using the ML method.”
High-Throughput Genomic Data in Systematics and Phylogenetics (2013, methodology): “Iterative methods for improving alignment quality may also reduce error for highly divergent sequences (e.g., SATé; Liu et al. 2012).”