@inbook{11bc0f9be59f4e98bfbe2fdca82fcfeb,
title = "Large-scale multiple sequence alignment and tree estimation using sat{\'e}",
abstract = "SAT{\'e} is a method for estimating multiple sequence alignments and trees that has been shown to produce highly accurate results for datasets with large numbers of sequences. Running SAT{\'e} using its default settings is very simple, but improved accuracy can be obtained by modifying its algorithmic parameters. We provide a detailed introduction to the algorithmic approach used by SAT{\'e}, and instructions for running a SAT{\'e} analysis using the GUI under default settings. We also provide a discussion of how to modify these settings to obtain improved results, and how to use SAT{\'e} in a phylogenetic analysis pipeline.",
keywords = "Gene tree estimation, Maximum likelihood, Multiple sequence alignment, Phylogenetics, Phylogenomics, SAT{\'e}, Species tree estimation",
author = "Kevin Liu and Tandy Warnow",
year = "2014",
doi = "10.1007/978-1-62703-646-7_15",
language = "English (US)",
isbn = "9781627036450",
series = "Methods in Molecular Biology",
publisher = "Humana Press Inc.",
pages = "219--244",
booktitle = "Multiple Sequence Alignment Methods",
}