Evolview v2: an online visualization and management tool for customized and annotated phylogenetic trees

被引：552
作者：
He, Zilong [1 ,2 ]
Zhang, Huangkai [1 ,2 ]
Gao, Shenghan [1 ]
Lercher, Martin J. [3 ,4 ]
Chen, Wei-Hua [1 ,5 ,6 ]
Hu, Songnian [1 ,2 ]
机构：
[1] Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, 7 Beitucheng West Rd, Beijing 100029, Peoples R China
[2] Univ Chinese Acad Sci, Beijing 100049, Peoples R China
[3] Univ Dusseldorf, Inst Comp Sci, D-40225 Dusseldorf, Germany
[4] Univ Dusseldorf, Cluster Excellence Plant Sci CEPLAS, D-40225 Dusseldorf, Germany
[5] Chinese Acad Sci, Beijing Inst Genom, BIG Data Ctr, 7 Beitucheng West Rd, Beijing 100029, Peoples R China
[6] Univ Geneva, Sch Med, Dept Genet Med & Dev, CH-1211 Geneva, Switzerland
来源：
NUCLEIC ACIDS RESEARCH | 2016年 / 44卷 / W1期
关键词：
GENE-TRANSFER; EVOLUTION; GENOME; INTEGRATION; FAMILY; LIFE; WEB;
D O I：
10.1093/nar/gkw370
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
Evolview is an online visualization and management tool for customized and annotated phylogenetic trees. It allows users to visualize phylogenetic trees in various formats, customize the trees through built-in functions and user-supplied datasets and export the customization results to publication-ready figures. Its 'dataset system' contains not only the data to be visualized on the tree, but also 'modifiers' that control various aspects of the graphical annotation. Evolview is a single-page application (like Gmail); its carefully designed interface allows users to upload, visualize, manipulate and manage trees and datasets all in a single webpage. Developments since the last public release include a modern dataset editor with keyword highlighting functionality, seven newly added types of annotation datasets, collaboration support that allows users to share their trees and datasets and various improvements of the web interface and performance. In addition, we included eleven new 'Demo' trees to demonstrate the basic functionalities of Evolview, and five new 'Showcase' trees inspired by publications to showcase the power of Evolview in producing publication-ready figures. Evolview is freely available at: http://www.evolgenius.info/evolview/.
引用
收藏
页码：W236 / W241
页数：6
相关论文
共 22 条
[1]   Dissecting Vancomycin-Intermediate Resistance in Staphylococcus aureus Using Genome-Wide Association [J].
Alam, Md Tauqeer ;
Petit, Robert A., III ;
Crispell, Emily K. ;
Thornton, Timothy A. ;
Conneely, Karen N. ;
Jiang, Yunxuan ;
Satola, Sarah W. ;
Read, Timothy D. .
GENOME BIOLOGY AND EVOLUTION, 2014, 6 (05) :1174-1185
[2]   T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks [J].
Alix, Boc ;
Boubacar, Diallo Alpha ;
Vladimir, Makarenkov .
NUCLEIC ACIDS RESEARCH, 2012, 40 (W1) :W573-W579
[3]   Treelink: data integration, clustering and visualization of phylogenetic trees [J].
Allende, Christian ;
Sohn, Erik ;
Little, Cedric .
BMC BIOINFORMATICS, 2015, 16
[4]  
[Anonymous], CURR PROTOC BIOINFOR
[5]   Phylogenetic reconstruction and lateral gene transfer [J].
Bapteste, E ;
Boucher, Y ;
Leigh, J ;
Doolittle, WF .
TRENDS IN MICROBIOLOGY, 2004, 12 (09) :406-411
[6]   Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances [J].
Chen, Wei-Hua ;
van Noort, Vera ;
Lluch-Senar, Maria ;
Hennrich, Marco L. ;
Wodke, Judith A. H. ;
Yus, Eva ;
Alibes, Andreu ;
Roma, Guglielmo ;
Mende, Daniel R. ;
Pesavento, Christina ;
Typas, Athanasios ;
Gavin, Anne-Claude ;
Serrano, Luis ;
Bork, Peer .
NUCLEIC ACIDS RESEARCH, 2016, 44 (03) :1192-1202
[7]   A High Through-put Platform for Recombinant Antibodies to Folded Proteins [J].
Hornsby, Michael ;
Paduch, Marcin ;
Miersch, Shane ;
Saeaef, Annika ;
Matsuguchi, Tet ;
Lee, Brian ;
Wypisniak, Karolina ;
Doak, Allison ;
King, Daniel ;
Usatyuk, Svitlana ;
Perry, Kimberly ;
Lu, Vince ;
Thomas, William ;
Luke, Judy ;
Goodman, Jay ;
Hoey, Robert J. ;
Lai, Darson ;
Griffin, Carly ;
Li, Zhijian ;
Vizeacoumar, Franco J. ;
Dong, Debbie ;
Campbell, Elliot ;
Anderson, Stephen ;
Zhong, Nan ;
Graeslund, Susanne ;
Koide, Shohei ;
Moffat, Jason ;
Sidhu, Sachdev ;
Kossiakoff, Anthony ;
Wells, James .
MOLECULAR & CELLULAR PROTEOMICS, 2015, 14 (10) :2833-2847
[8]   ETE: a python']python Environment for Tree Exploration [J].
Huerta-Cepas, Jaime ;
Dopazo, Joaquin ;
Gabaldon, Toni .
BMC BIOINFORMATICS, 2010, 11
[9]   Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks [J].
Huson, Daniel H. ;
Scornavacca, Celine .
SYSTEMATIC BIOLOGY, 2012, 61 (06) :1061-1067
[10]   PhyloWidget: web-based visualizations for the tree of life [J].
Jordan, Gregory E. ;
Piel, William H. .
BIOINFORMATICS, 2008, 24 (14) :1641-1642
123