Visualization of multiple alignments, phylogenies and gene family evolution

James B. Procter; Julie Thompson; Ivica Letunic; Chris Creevey; Fabrice Jossinet; Geoffrey J. Barton

doi:10.1038/NMETH.1434

Visualization of multiple alignments, phylogenies and gene family evolution

James B. Procter, Julie Thompson, Ivica Letunic, Chris Creevey, Fabrice Jossinet, Geoffrey J. Barton

Computational Biology

Research output: Contribution to journal › Review article

52 Citations (Scopus)

Abstract

Software for visualizing sequence alignments and trees are essential tools for life scientists. In this review, we describe the major features and capabilities of a selection of stand-alone and web-based applications useful when investigating the function and evolution of a gene family. These range from simple viewers, to systems that provide sophisticated editing and analysis functions. We conclude with a discussion of the challenges that these tools now face due to the flood of next generation sequence data and the increasingly complex network of bioinformatics information sources.

Original language	English
Pages (from-to)	S16-S25
Number of pages	10
Journal	Nature Methods
Volume	7
Issue number	3
DOIs	https://doi.org/10.1038/NMETH.1434
Publication status	Published - 1 Mar 2010

Keywords

SEQUENCE ALIGNMENT
RESIDUE CONSERVATION
HYPERBOLIC SPACE
TREES
DATABASE
INFORMATION
ONTOLOGY
DISPLAY
TOOL
PREDICTION

Access to Document

10.1038/NMETH.1434

Cite this

Procter, J. B., Thompson, J., Letunic, I., Creevey, C., Jossinet, F., & Barton, G. J. (2010). Visualization of multiple alignments, phylogenies and gene family evolution. Nature Methods, 7(3), S16-S25. https://doi.org/10.1038/NMETH.1434

@article{cb8e8a34a4444bd397ccdd6166b4cc1b,

title = "Visualization of multiple alignments, phylogenies and gene family evolution",

abstract = "Software for visualizing sequence alignments and trees are essential tools for life scientists. In this review, we describe the major features and capabilities of a selection of stand-alone and web-based applications useful when investigating the function and evolution of a gene family. These range from simple viewers, to systems that provide sophisticated editing and analysis functions. We conclude with a discussion of the challenges that these tools now face due to the flood of next generation sequence data and the increasingly complex network of bioinformatics information sources.",

keywords = "SEQUENCE ALIGNMENT, RESIDUE CONSERVATION, HYPERBOLIC SPACE, TREES, DATABASE, INFORMATION, ONTOLOGY, DISPLAY, TOOL, PREDICTION",

author = "Procter, {James B.} and Julie Thompson and Ivica Letunic and Chris Creevey and Fabrice Jossinet and Barton, {Geoffrey J.}",

year = "2010",

month = mar,

day = "1",

doi = "10.1038/NMETH.1434",

language = "English",

volume = "7",

pages = "S16--S25",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Nature Publishing Group",

number = "3",

}

TY - JOUR

T1 - Visualization of multiple alignments, phylogenies and gene family evolution

AU - Procter, James B.

AU - Thompson, Julie

AU - Letunic, Ivica

AU - Creevey, Chris

AU - Jossinet, Fabrice

AU - Barton, Geoffrey J.

PY - 2010/3/1

Y1 - 2010/3/1

N2 - Software for visualizing sequence alignments and trees are essential tools for life scientists. In this review, we describe the major features and capabilities of a selection of stand-alone and web-based applications useful when investigating the function and evolution of a gene family. These range from simple viewers, to systems that provide sophisticated editing and analysis functions. We conclude with a discussion of the challenges that these tools now face due to the flood of next generation sequence data and the increasingly complex network of bioinformatics information sources.

AB - Software for visualizing sequence alignments and trees are essential tools for life scientists. In this review, we describe the major features and capabilities of a selection of stand-alone and web-based applications useful when investigating the function and evolution of a gene family. These range from simple viewers, to systems that provide sophisticated editing and analysis functions. We conclude with a discussion of the challenges that these tools now face due to the flood of next generation sequence data and the increasingly complex network of bioinformatics information sources.

KW - SEQUENCE ALIGNMENT

KW - RESIDUE CONSERVATION

KW - HYPERBOLIC SPACE

KW - TREES

KW - DATABASE

KW - INFORMATION

KW - ONTOLOGY

KW - DISPLAY

KW - TOOL

KW - PREDICTION

U2 - 10.1038/NMETH.1434

DO - 10.1038/NMETH.1434

M3 - Review article

VL - 7

SP - S16-S25

JO - Nature Methods

JF - Nature Methods

SN - 1548-7091

IS - 3

ER -