Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees

Kevin Liu, Sindhu Raghavan, Serita Nelesen, C. Randal Linder, Tandy Warnow

Research output: Contribution to journalArticle

Abstract

Inferring an accurate evolutionary tree of life requires high-quality alignments of molecular sequence data sets from large numbers of species. However, this task is often difficult, slow, and idiosyncratic, especially when the sequences are highly diverged or include high rates of insertions and deletions (collectively known as indels). We present SATé (simultaneous alignment and tree estimation), an automated method to quickly and accurately estimate both DNA alignments and trees with the maximum likelihood criterion. In our study, it improved tree and alignment accuracy compared to the best two-phase methods currently available for data sets of up to 1000 sequences, showing that coestimation can be both rapid and accurate in phylogenetic studies.

Original languageEnglish (US)
Pages (from-to)1561-1564
Number of pages4
JournalScience
Volume324
Issue number5934
DOIs
StatePublished - Jun 19 2009

Fingerprint

Sequence Alignment
Molecular Sequence Data
DNA
Datasets

ASJC Scopus subject areas

  • General

Cite this

Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. / Liu, Kevin; Raghavan, Sindhu; Nelesen, Serita; Linder, C. Randal; Warnow, Tandy.

In: Science, Vol. 324, No. 5934, 19.06.2009, p. 1561-1564.

Research output: Contribution to journalArticle

Liu, Kevin ; Raghavan, Sindhu ; Nelesen, Serita ; Linder, C. Randal ; Warnow, Tandy. / Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. In: Science. 2009 ; Vol. 324, No. 5934. pp. 1561-1564.
@article{156328f156a047f3940436238ddfff02,
title = "Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees",
abstract = "Inferring an accurate evolutionary tree of life requires high-quality alignments of molecular sequence data sets from large numbers of species. However, this task is often difficult, slow, and idiosyncratic, especially when the sequences are highly diverged or include high rates of insertions and deletions (collectively known as indels). We present SAT{\'e} (simultaneous alignment and tree estimation), an automated method to quickly and accurately estimate both DNA alignments and trees with the maximum likelihood criterion. In our study, it improved tree and alignment accuracy compared to the best two-phase methods currently available for data sets of up to 1000 sequences, showing that coestimation can be both rapid and accurate in phylogenetic studies.",
author = "Kevin Liu and Sindhu Raghavan and Serita Nelesen and Linder, {C. Randal} and Tandy Warnow",
year = "2009",
month = "6",
day = "19",
doi = "10.1126/science.1171243",
language = "English (US)",
volume = "324",
pages = "1561--1564",
journal = "Science",
issn = "0036-8075",
publisher = "American Association for the Advancement of Science",
number = "5934",

}

TY - JOUR

T1 - Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees

AU - Liu, Kevin

AU - Raghavan, Sindhu

AU - Nelesen, Serita

AU - Linder, C. Randal

AU - Warnow, Tandy

PY - 2009/6/19

Y1 - 2009/6/19

N2 - Inferring an accurate evolutionary tree of life requires high-quality alignments of molecular sequence data sets from large numbers of species. However, this task is often difficult, slow, and idiosyncratic, especially when the sequences are highly diverged or include high rates of insertions and deletions (collectively known as indels). We present SATé (simultaneous alignment and tree estimation), an automated method to quickly and accurately estimate both DNA alignments and trees with the maximum likelihood criterion. In our study, it improved tree and alignment accuracy compared to the best two-phase methods currently available for data sets of up to 1000 sequences, showing that coestimation can be both rapid and accurate in phylogenetic studies.

AB - Inferring an accurate evolutionary tree of life requires high-quality alignments of molecular sequence data sets from large numbers of species. However, this task is often difficult, slow, and idiosyncratic, especially when the sequences are highly diverged or include high rates of insertions and deletions (collectively known as indels). We present SATé (simultaneous alignment and tree estimation), an automated method to quickly and accurately estimate both DNA alignments and trees with the maximum likelihood criterion. In our study, it improved tree and alignment accuracy compared to the best two-phase methods currently available for data sets of up to 1000 sequences, showing that coestimation can be both rapid and accurate in phylogenetic studies.

UR - http://www.scopus.com/inward/record.url?scp=67649240664&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=67649240664&partnerID=8YFLogxK

U2 - 10.1126/science.1171243

DO - 10.1126/science.1171243

M3 - Article

C2 - 19541996

AN - SCOPUS:67649240664

VL - 324

SP - 1561

EP - 1564

JO - Science

JF - Science

SN - 0036-8075

IS - 5934

ER -