Bioinformatics Vol. 17 no. 4 2001
Pages 383-384
© 2001 Oxford University Press
Applications Note |
ATV: display and manipulation of annotated phylogenetic trees
Howard Hughes Medical Institute, Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
Received on November 1, 2000
; revised on December 19, 2000
; accepted on December 21, 2000
Summary: A Tree Viewer (ATV) is a Java tool for the display and manipulation of annotated phylogenetic trees. It can be utilized both as a standalone application and as an applet in a web browser.
Availability: ATV is available via WWW at http://www.genetics.wustl.edu/eddy/atv/ and via FTP at ftp://ftp.genetics.wustl.edu/pub/eddy/software/forester.tar.Z
Contact: eddy{at}genetics.wustl.edu
![]()
CiteULike
Connotea
Del.icio.us What's this?
This article has been cited by other articles:
![]() |
J. Muller, D. Szklarczyk, P. Julien, I. Letunic, A. Roth, M. Kuhn, S. Powell, C. von Mering, T. Doerks, L. J. Jensen, et al. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations Nucleic Acids Res., November 9, 2009; (2009) gkp951v1. [Abstract] [Full Text] [PDF] |
||||
![]() |
G. Ostlund, T. Schmitt, K. Forslund, T. Kostler, D. N. Messina, S. Roopra, O. Frings, and E. L. L. Sonnhammer InParanoid 7: new algorithms and tools for eukaryotic orthology analysis Nucleic Acids Res., November 5, 2009; (2009) gkp931v1. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. Schluter, A. Real-Chicharro, T. Gabaldon, F. Sanchez-Jimenez, and A. Pujol PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome Nucleic Acids Res., November 5, 2009; (2009) gkp935v1. [Abstract] [Full Text] [PDF] |
||||
![]() |
T.-H. Lee, Y.-K. Kim, T. T. M. Pham, S. I. Song, J.-K. Kim, K. Y. Kang, G. An, K.-H. Jung, D. W. Galbraith, M. Kim, et al. RiceArrayNet: A Database for Correlating Gene Expression from Transcriptome Profiling, and Its Application to the Analysis of Coexpressed Genes in Rice Plant Physiology, September 1, 2009; 151(1): 16 - 33. [Abstract] [Full Text] [PDF] |
||||
![]() |
R. Gouveia-Oliveira, F. S. Roque, R. Wernersson, T. Sicheritz-Ponten, P. W. Sackett, A. Molgaard, and A. G. Pedersen InterMap3D: predicting and visualizing co-evolving protein residues Bioinformatics, August 1, 2009; 25(15): 1963 - 1965. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Sankararaman, B. Kolaczkowski, and K. Sjolander INTREPID: a web server for prediction of functionally important residues by evolutionary analysis Nucleic Acids Res., July 1, 2009; 37(suppl_2): W390 - W395. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Thongjuea, V. Ruanjaichon, R. Bruskiewich, and A. Vanavichit RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome Nucleic Acids Res., January 1, 2009; 37(suppl_1): D996 - D1000. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. Yilmaz, M. Y. Nishiyama Jr., B. G. Fuentes, G. M. Souza, D. Janies, J. Gray, and E. Grotewold GRASSIUS: A Platform for Comparative Regulatory Genomics across the Grasses Plant Physiology, January 1, 2009; 149(1): 171 - 180. [Abstract] [Full Text] [PDF] |
||||
![]() |
G. E. Jordan and W. H. Piel PhyloWidget: web-based visualizations for the tree of life Bioinformatics, July 15, 2008; 24(14): 1641 - 1642. [Abstract] [Full Text] [PDF] |
||||
![]() |
K. Katoh and H. Toh Recent developments in the MAFFT multiple sequence alignment program Brief Bioinform, July 1, 2008; 9(4): 286 - 298. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. Dereeper, V. Guignon, G. Blanc, S. Audic, S. Buffet, F. Chevenet, J.-F. Dufayard, S. Guindon, V. Lefort, M. Lescot, et al. Phylogeny.fr: robust phylogenetic analysis for the non-specialist Nucleic Acids Res., July 1, 2008; 36(suppl_2): W465 - W469. [Abstract] [Full Text] [PDF] |
||||
![]() |
N. O'Toole, M. Hattori, C. Andres, K. Iida, C. Lurin, C. Schmitz-Linneweber, M. Sugita, and I. Small On the Expansion of the Pentatricopeptide Repeat Gene Family in Plants Mol. Biol. Evol., June 1, 2008; 25(6): 1120 - 1128. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Wanchana, S. Thongjuea, V. J. Ulat, M. Anacleto, R. Mauleon, M. Conte, M. Rouard, M. Ruiz, N. Krishnamurthy, K. Sjolander, et al. The Generation Challenge Programme comparative plant stress-responsive gene catalogue Nucleic Acids Res., January 11, 2008; 36(suppl_1): D943 - D946. [Abstract] [Full Text] [PDF] |
||||
![]() |
N. J. Tourasse and A.-B. Kolsto SuperCAT: a supertree database for combined and integrative multilocus sequence typing analysis of the Bacillus cereus group of bacteria (including B. cereus, B. anthracis and B. thuringiensis) Nucleic Acids Res., January 11, 2008; 36(suppl_1): D461 - D468. [Abstract] [Full Text] [PDF] |
||||
![]() |
F. Enault, R. Fremez, E. Baranowski, and T. Faraut Alvira: comparative genomics of viral strains Bioinformatics, August 15, 2007; 23(16): 2178 - 2179. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. G. Glanville, D. Kirshner, N. Krishnamurthy, and K. Sjolander Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis Nucleic Acids Res., July 13, 2007; 35(suppl_2): W27 - W32. [Abstract] [Full Text] [PDF] |
||||
![]() |
X.-C. Zhang, X. Wu, S. Findley, J. Wan, M. Libault, H. T. Nguyen, S. B. Cannon, and G. Stacey Molecular Evolution of Lysin Motif-Type Receptor-Like Kinases in Plants Plant Physiology, June 1, 2007; 144(2): 623 - 636. [Abstract] [Full Text] [PDF] |
||||
![]() |
R. Fremez, T. Faraut, G. Fichant, J. Gouzy, and Y. Quentin Phylogenetic exploration of bacterial genomic rearrangements Bioinformatics, May 1, 2007; 23(9): 1172 - 1174. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Faure, J. Higgins, A. Turner, and D. A. Laurie The FLOWERING LOCUS T-Like Gene Family in Barley (Hordeum vulgare) Genetics, May 1, 2007; 176(1): 599 - 609. [Abstract] [Full Text] [PDF] |
||||
![]() |
K. Hanekamp, U. Bohnebeck, B. Beszteri, and K. Valentin PhyloGena a user-friendly system for automated phylogenetic annotation of unknown sequences Bioinformatics, April 1, 2007; 23(7): 793 - 801. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Richardt, D. Lang, R. Reski, W. Frank, and S. A. Rensing PlanTAPDB, a Phylogeny-Based Resource of Plant Transcription-Associated Proteins Plant Physiology, April 1, 2007; 143(4): 1452 - 1466. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Gu, I. Anderson, V. Kunin, M. Cipriano, S. Minovitsky, G. Weber, N. Amenta, B. Hamann, and I. Dubchak TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities Bioinformatics, March 15, 2007; 23(6): 764 - 766. [Abstract] [Full Text] [PDF] |
||||
![]() |
Q. Ren, K. Chen, and I. T. Paulsen TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels Nucleic Acids Res., January 12, 2007; 35(suppl_1): D274 - D279. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. Schluter, S. Fourcade, E. Domenech-Estevez, T. Gabaldon, J. Huerta-Cepas, G. Berthommier, R. Ripp, R. J. A. Wanders, O. Poch, and A. Pujol PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease Nucleic Acids Res., January 12, 2007; 35(suppl_1): D815 - D822. [Abstract] [Full Text] [PDF] |
||||
![]() |
I. Letunic and P. Bork Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation Bioinformatics, January 1, 2007; 23(1): 127 - 128. [Abstract] [Full Text] [PDF] |
||||
![]() |
D. H. Morgan, D. M. Kristensen, D. Mittelman, and O. Lichtarge ET viewer: an application for predicting and visualizing functional sites in protein structures Bioinformatics, August 15, 2006; 22(16): 2049 - 2050. [Abstract] [Full Text] [PDF] |
||||
![]() |
A.-M. Arigon, G. Perriere, and M. Gouy HoSeqI: automated homologous sequence identification in gene family databases Bioinformatics, July 15, 2006; 22(14): 1786 - 1787. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. Rampp, T. Soddemann, and H. Lederer The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W15 - W19. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. Flaus, D. M. A. Martin, G. J. Barton, and T. Owen-Hughes Identification of multiple distinct Snf2 subfamilies with conserved structural motifs Nucleic Acids Res., May 31, 2006; 34(10): 2887 - 2905. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. J. Sanderson Paloverde: an OpenGL 3D phylogeny browser Bioinformatics, April 15, 2006; 22(8): 1004 - 1006. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. H. Saier Jr, C. V. Tran, and R. D. Barabote TCDB: the Transporter Classification Database for membrane transport protein analyses and information Nucleic Acids Res., January 1, 2006; 34(suppl_1): D181 - D186. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Whelan, P. I. W. de Bakker, E. Quevillon, N. Rodriguez, and N. Goldman PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees Nucleic Acids Res., January 1, 2006; 34(suppl_1): D327 - D331. [Abstract] [Full Text] [PDF] |
||||
![]() |
H. Li, A. Coghlan, J. Ruan, L. J. Coin, J.-K. Heriche, L. Osmotherly, R. Li, T. Liu, Z. Zhang, L. Bolund, et al. TreeFam: a curated database of phylogenetic trees of animal gene families Nucleic Acids Res., January 1, 2006; 34(suppl_1): D572 - D580. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Hartmann, D. Lu, J. Phillips, and T. J. Vision Phytome: a platform for plant comparative genomics Nucleic Acids Res., January 1, 2006; 34(suppl_1): D724 - D730. [Abstract] [Full Text] [PDF] |
||||
![]() |
C.-Y. Lin, F.-K. Lin, C. H. Lin, L.-W. Lai, H.-J. Hsu, S.-H. Chen, and C. A. Hsiung POWER: PhylOgenetic WEb Repeater--an integrated and user-optimized framework for biomolecular phylogenetic analysis Nucleic Acids Res., July 1, 2005; 33(suppl_2): W553 - W556. [Abstract] [Full Text] [PDF] |
||||
![]() |
S. Guindon, F. Lethiec, P. Duroux, and O. Gascuel PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference Nucleic Acids Res., July 1, 2005; 33(suppl_2): W557 - W559. [Abstract] [Full Text] [PDF] |
||||
![]() |
D. M. Aanensen and B. G. Spratt The multilocus sequence typing network: mlst.net Nucleic Acids Res., July 1, 2005; 33(suppl_2): W728 - W733. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. Friedrich, T. Dandekar, M. Wolf, and T. Muller ProfDist: a tool for the construction of large phylogenetic trees based on profile distances Bioinformatics, May 1, 2005; 21(9): 2108 - 2109. [Abstract] [Full Text] [PDF] |
||||
![]() |
Q. C. Truong-Bolduc, P. M. Dunman, J. Strahilevitz, S. J. Projan, and D. C. Hooper MgrA Is a Multiple Regulator of Two New Efflux Pumps in Staphylococcus aureus J. Bacteriol., April 1, 2005; 187(7): 2395 - 2405. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. G. Greslebin, E. M. Hansen, L. M. Winton, and M. Rajchenberg Phytophthora species from declining Austrocedrus chilensis forests in Patagonia, Argentina Mycologia, January 1, 2005; 97(1): 218 - 228. [Abstract] [Full Text] [PDF] |
||||
![]() |
R. Homayouni, K. Heinrich, L. Wei, and M. W. Berry Gene clustering by Latent Semantic Indexing of MEDLINE abstracts Bioinformatics, January 1, 2005; 21(1): 104 - 115. [Abstract] [Full Text] [PDF] |
||||
![]() |
C. S. Janssen, R. S. Phillips, C. M. R. Turner, and M. P. Barrett Plasmodium interspersed repeats: the major multigene superfamily of malaria parasites Nucleic Acids Res., October 26, 2004; 32(19): 5712 - 5720. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. E. Hill, S. L. Penny, K. G. Crowell, S. H. Goh, and S. M. Hemmingsen cpnDB: A Chaperonin Sequence Database Genome Res., August 1, 2004; 14(8): 1669 - 1675. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. Wuyts, G. Perriere, and Y. Van de Peer The European ribosomal RNA database Nucleic Acids Res., January 1, 2004; 32(90001): D101 - 103. [Abstract] [Full Text] [PDF] |
||||
![]() |
D. Ruau, J. Duarte, T. Ourjdal, G. Perriere, V. Laudet, and M. Robinson-Rechavi Update of NUREBASE: nuclear hormone receptor functional genomics Nucleic Acids Res., January 1, 2004; 32(90001): D165 - 167. [Abstract] [Full Text] [PDF] |
||||
![]() |
G. Perriere, C. Combet, S. Penel, C. Blanchet, J. Thioulouse, C. Geourjon, J. Grassot, C. Charavay, M. Gouy, L. Duret, et al. Integrated databanks access and sequence/structure analysis services at the PBIL Nucleic Acids Res., July 1, 2003; 31(13): 3393 - 3399. [Abstract] [Full Text] [PDF] |
||||
![]() |
N. Bray and L. Pachter MAVID multiple alignment server Nucleic Acids Res., July 1, 2003; 31(13): 3525 - 3526. [Abstract] [Full Text] [PDF] |
||||
![]() |
G. Devulder, G. Perriere, F. Baty, and J. P. Flandrois BIBI, a Bioinformatics Bacterial Identification Tool J. Clin. Microbiol., April 1, 2003; 41(4): 1785 - 1787. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. Grassot, G. Mouchiroud, and G. Perriere RTKdb: database of receptor tyrosine kinase Nucleic Acids Res., January 1, 2003; 31(1): 353 - 358. [Abstract] [Full Text] [PDF] |
||||









