Efficient comparative phylogenetics on large trees

被引：364

作者：

Louca, Stilianos ^{[1
,2
]}

Doebeli, Michael ^{[1
,2
,3
]}

机构：

[1] Univ British Columbia, Biodivers Res Ctr, Vancouver, BC V6T 1Z4, Canada

[2] Univ British Columbia, Dept Zool, Vancouver, BC V6T 1Z4, Canada

[3] Univ British Columbia, Dept Math, Vancouver, BC V6T 1Z4, Canada

来源：

BIOINFORMATICS | 2018年 / 34卷 / 06期

基金：

加拿大自然科学与工程研究理事会;

关键词：

TOOLS;

D O I：

10.1093/bioinformatics/btx701

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: Biodiversity databases now comprise hundreds of thousands of sequences and trait records. For example, the Open Tree of Life includes over 1 491 000 metazoan and over 300 000 bacterial taxa. These data provide unique opportunities for analysis of phylogenetic trait distribution and reconstruction of ancestral biodiversity. However, existing tools for comparative phylogenetics scale poorly to such large trees, to the point of being almost unusable. Results: Here we present a new R package, named 'castor', for comparative phylogenetics on large trees comprising millions of tips. On large trees castor is often 100-1000 times faster than existing tools.

引用

页码：1053 / 1055

页数：3

共 11 条

[1] Phyx: phylogenetic tools for unix [J].

Brown, Joseph W. ;

Walker, Joseph F. ;

Smith, Stephen A. .

BIOINFORMATICS, 2017, 33 (12) :1886-1888

[2] Diversitree: comparative phylogenetic analyses of diversification in R [J].

FitzJohn, Richard G. .

METHODS IN ECOLOGY AND EVOLUTION, 2012, 3 (06) :1084-1092

[3] GEIGER: investigating evolutionary radiations [J].

Harmon, Luke J. ;

Weir, Jason T. ;

Brock, Chad D. ;

Glor, Richard E. ;

Challenger, Wendell .

BIOINFORMATICS, 2008, 24 (01) :129-131

[4] Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology [J].

Karp, Peter D. ;

Paley, Suzanne M. ;

Krummenacker, Markus ;

Latendresse, Mario ;

Dale, Joseph M. ;

Lee, Thomas J. ;

Kaipa, Pallavi ;

Gilham, Fred ;

Spaulding, Aaron ;

Popescu, Liviu ;

Altman, Tomer ;

Paulsen, Ian ;

Keseler, Ingrid M. ;

Caspi, Ron .

BRIEFINGS IN BIOINFORMATICS, 2010, 11 (01) :40-79

[5] SQUARED-CHANGE PARSIMONY RECONSTRUCTIONS OF ANCESTRAL STATES FOR CONTINUOUS-VALUED CHARACTERS ON A PHYLOGENETIC TREE [J].

MADDISON, WP .

SYSTEMATIC ZOOLOGY, 1991, 40 (03) :304-314

[6]

Paradis E, 2004, BIOINFORMATICS, V20, P289, DOI [10.1093/bioinformatics/btg412, 10.1093/bioinformatics/bty633]

[7] The SILVA ribosomal RNA gene database project: improved data processing and web-based tools [J].

Quast, Christian ;

Pruesse, Elmar ;

Yilmaz, Pelin ;

Gerken, Jan ;

Schweer, Timmy ;

Yarza, Pablo ;

Peplies, Joerg ;

Gloeckner, Frank Oliver .

NUCLEIC ACIDS RESEARCH, 2013, 41 (D1) :D590-D596

[8] phytools: an R package for phylogenetic comparative biology (and other things) [J].

Revell, Liam J. .

METHODS IN ECOLOGY AND EVOLUTION, 2012, 3 (02) :217-223

[9] phangorn: phylogenetic analysis in R [J].

Schliep, Klaus Peter .

BIOINFORMATICS, 2011, 27 (04) :592-593

[10]

YANG ZH, 1995, GENETICS, V141, P1641

← 1 2 →