Dendroscope

Dendroscope: An interactive viewer for large phylogenetic trees. BACKGROUND: Research in evolution requires software for visualizing and editing phylogenetic trees, for increasingly very large datasets, such as arise in expression analysis or metagenomics, for example. It would be desirable to have a program that provides these services in an efficient and user-friendly way, and that can be easily installed and run on all major operating systems. Although a large number of tree visualization tools are freely available, some as a part of more comprehensive analysis packages, all have drawbacks in one or more domains. They either lack some of the standard tree visualization techniques or basic graphics and editing features, or they are restricted to small trees containing only tens of thousands of taxa. Moreover, many programs are difficult to install or are not available for all common operating systems. RESULTS: We have developed a new program, Dendroscope, for the interactive visualization and navigation of phylogenetic trees. The program provides all standard tree visualizations and is optimized to run interactively on trees containing hundreds of thousands of taxa. The program provides tree editing and graphics export capabilities. To support the inspection of large trees, Dendroscope offers a magnification tool. The software is written in Java 1.4 and installers are provided for Linux/Unix, MacOS X and Windows XP. CONCLUSION: Dendroscope is a user-friendly program for visualizing and navigating phylogenetic trees, for both small and large datasets.


References in zbMATH (referenced in 12 articles )

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  1. Warnow, Tandy (ed.): Bioinformatics and phylogenetics. Seminal contributions of Bernard Moret (2019)
  2. van Iersel, Leo; Kelk, Steven; Stamoulis, Georgios; Stougie, Leen; Boes, Olivier: On unrooted and root-uncertain variants of several well-known phylogenetic network problems (2018)
  3. Wicke, Kristina; Fischer, Mareike: Phylogenetic diversity and biodiversity indices on phylogenetic networks (2018)
  4. Huber, Katharina T.; van Iersel, Leo; Moulton, Vincent; Scornavacca, Celine; Wu, Taoyang: Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets (2017)
  5. Keith, Jonathan M. (ed.): Bioinformatics. Volume II: structure, function, and applications (2017)
  6. Kelk, Steven; van Iersel, Leo; Scornavacca, Celine; Weller, Mathias: Phylogenetic incongruence through the lens of monadic second order logic (2016)
  7. Fischer, Mareike; van Iersel, Leo; Kelk, Steven; Scornavacca, Celine: On computing the maximum parsimony score of a phylogenetic network (2015)
  8. Steel, Mike; Linz, Simone; Huson, Daniel H.; Sanderson, Michael J.: Identifying a species tree subject to random lateral gene transfer (2013)
  9. Aydın, Burcu; Pataki, Gábor; Wang, Haonan; Ladha, Alim; Bullitt, Elizabeth; Marron, J. S.: Visualizing the structure of large trees (2011)
  10. van Iersel, Leo; Kelk, Steven: When two trees go to war (2011)
  11. Stöver, Ben C.; Müller, Kai F.: Treegraph 2: combining and visualizing evidence from different phylogenetic analyses (2010) ioport
  12. Huson, Daniel H.; Richter, Daniel C.; Rausch, Christian; Dezulian, Tobias; Franz, Markus; Rupp, Regula: Dendroscope: An interactive viewer for large phylogenetic trees (2007) ioport