ArticleMethods in molecular biology (Clifton, N.J.)2014
Large-scale multiple sequence alignment and tree estimation using SATé.
Article in Methods in molecular biology (Clifton, N.J.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- An nf-core framework for the systematic comparison of alternative modeling tools: the multiple sequence alignment case study.NAR genomics and bioinformatics · 2025Article
- Expanding the Riboglow-FLIM Toolbox with Different Fluorescence Lifetime-Producing RNA Tags.Biochemistry · 2025Article
- DiMA: sequence diversity dynamics analyser for viruses.Briefings in bioinformatics · 2024Article
- The Cambrian cirratuliformProceedings. Biological sciences · 2023Article
- cpxDeepMSA: A Deep Cascade Algorithm for Constructing Multiple Sequence Alignments of Protein-Protein Interactions.International journal of molecular sciences · 2022Article
- PhyloFunDB: A Pipeline to Create and Update Functional Gene Taxonomic Databases.Microorganisms · 2022Article
- Efficient merging of genome profile alignments.Bioinformatics (Oxford, England) · 2019Article
- Evolutionary dynamics and molecular epidemiology ofVirus evolution · 2019Article
- Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses.Briefings in bioinformatics · 2015Article
- The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.Genome biology · 2014Article
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Authors and funding
2 authors.
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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.
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