Large-scale multiple sequence alignment and tree estimation using saté

Kevin Liu, Tandy Warnow

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

SATé 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 SATé 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 SATé, and instructions for running a SATé 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 SATé in a phylogenetic analysis pipeline.

Original languageEnglish (US)
Title of host publicationMultiple Sequence Alignment Methods
PublisherHumana Press Inc.
Pages219-244
Number of pages26
ISBN (Print)9781627036450
DOIs
StatePublished - 2014
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume1079
ISSN (Print)1064-3745

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Keywords

  • Gene tree estimation
  • Maximum likelihood
  • Multiple sequence alignment
  • Phylogenetics
  • Phylogenomics
  • SATé
  • Species tree estimation

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Liu, K., & Warnow, T. (2014). Large-scale multiple sequence alignment and tree estimation using saté. In Multiple Sequence Alignment Methods (pp. 219-244). (Methods in Molecular Biology; Vol. 1079). Humana Press Inc.. https://doi.org/10.1007/978-1-62703-646-7_15