Cobweb: a Java applet for network exploration and visualisation

SUMMARY: Cobweb is a Java applet for real-time network visualization; its strength lies in enabling the interactive exploration of networks. Therefore, it allows new nodes to be interactively added to a network by querying a database on a server. The network constantly rearranges to provide the most meaningful topological view. AVAILABILITY: Cobweb is available under the GPLv3 and may be freely downloaded at http://bioinformatics.charite.de/cobweb.     

Tools for visualization and integration of intermediate sequencing results in large disease gene discovery projects

We describe two Java applets which are useful for insightful presentation of intermediate experimental data in gene discovery projects involving large scale sequencing. One of these applets provides a physical map of a genomic region and provides easy access to the second applet, which furnishes a detailed map of sequence contigs associated with clones on the physical map. In particular, the second applet displays all the known information about each contig, including the presence of exons, database homology `hits', repetitive elements and other features; the graphics are linked to other World Wide Web pages, providing detailed information on each feature. These applets should be useful to other research groups working on large sequencing projects.     

NIFAS: visual analysis of domain evolution in proteins

MOTIVATION: Multi-domain proteins have evolved by insertions or deletions of distinct protein domains. Tracing the history of a certain domain combination can be important for functional annotation of multi-domain proteins, and for understanding the function of individual domains. In order to analyze the evolutionary history of the domains in modular proteins it is desirable to inspect a phylogenetic tree based on sequence divergence with the modular architecture of the sequences superimposed on the tree. RESULT: A Java applet, NIFAS, that integrates graphical domain schematics for each sequence in an evolutionary tree was developed. NIFAS retrieves domain information from the Pfam database and uses CLUSTAL W to calculate a tree for a given Pfam domain. The tree can be displayed with symbolic bootstrap values, and to allow the user to focus on a part of the tree, the layout can be altered by swapping nodes, changing the outgroup, and showing/collapsing subtrees. NIFAS is integrated with the Pfam database and is accessible over the internet (http://www.cgr.ki.se/Pfam). As an example, we use NIFAS to analyze the evolution of domains in Protein Kinases C.     

MDB: the Metalloprotein Database and Browser at The Scripps Research Institute

The Metalloprotein Database and Browser (MDB; http://metallo.scripps.edu) at The Scripps Research Institute is a web-accessible resource for metalloprotein research. It offers the scientific community quantitative information on geometrical parameters of metal-binding sites in protein structures available from the Protein Data Bank (PDB). The MDB also offers analytical tools for the examination of trends or patterns in the indexed metal-binding sites. A user can perform interactive searches, metal-site structure visualization (via a Java applet), and analysis of the quantitative data by accessing the MDB through a web browser without requiring an external application or platform-dependent plugin. The MDB also has a non-interactive interface with which other web sites and network-aware applications can seamlessly incorporate data or statistical analysis results from metal-binding sites. The information contained in the MDB is periodically updated with automated algorithms that find and index metal sites from new protein structures released by the PDB.     

PfamAlyzer: domain-centric homology search

PfamAlyzer is a Java applet that enables exploration of Pfam domain architectures using a user-friendly graphical interface. It can search the UniProt protein database for a domain pattern. Domain patterns similar to the query are presented graphically by PfamAlyzer either in a ranked list or pinned to the tree of life. Such domain-centric homology search can assist identification of distant homologs with shared domain architecture. AVAILABILITY: PfamAlyzer has been integrated with the Pfam database and can be accessed at http://pfam.cgb.ki.se/pfamalyzer.     

DINAMO: interactive protein alignment and model building.

MOTIVATION: To facilitate the process of structure prediction by both comparative modeling and fold recognition, we describe DINAMO, an interactive protein alignment building and model evaluation tool that dynamically couples a multiple sequence alignment editor to a molecular graphics display. DINAMO allows the user to optimize the alignment and model to satisfy the known heuristics of protein structure by means of a set of analysis tools. The analysis tools return information to both the alignment editor and graphics model in the form of visual cues (color, shape), allowing for rapid evaluation. Several analysis tools may be employed, including residue conservation, residue properties (charge, hydrophobicity, volume), residue environmental preference, and secondary structure propensity. RESULTS: We demonstrate DINAMO by building a model for submission in the 3rd annual Critical Assessment of Techniques for Protein Structure Prediction (CASP3) contest. AVAILABILITY: DINAMO is freely available as a local application or Web-based Java applet at http://tito.ucsc.edu/dinamo     

ATV: display and manipulation of annotated phylogenetic trees

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.     

Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data,and the branching order in hominoidea

Summary A maximum likelihood method for inferring evolutionary trees from DNA sequence data was developed by Felsenstein (1981). In evaluating the extent to which the maximum likelihood tree is a significantly better representation of the true tree, it is important to estimate the variance of the difference between log likelihood of different tree topologies. Bootstrap resampling can be used for this purpose (Hasegawa et al. 1988; Hasegawa and Kishino 1989), but it imposes a great computation burden. To overcome this difficulty, we developed a new method for estimating the variance by expressing it explicitly.The method was applied to DNA sequence data from primates in order to evaluate the maximum likelihood branching order among Hominoidea. It was shown that, although the orangutan is convincingly placed as an outgroup of a human and African apes clade, the branching order among human, chimpanzee, and gorilla cannot be determined confidently from the DNA sequence data presently available when the evolutionary rate constancy is not assumed.     

treespace: Statistical exploration of landscapes of phylogenetic trees

The increasing availability of large genomic data sets as well as the advent of Bayesian phylogenetics facilitates the investigation of phylogenetic incongruence, which can result in the impossibility of representing phylogenetic relationships using a single tree. While sometimes considered as a nuisance, phylogenetic incongruence can also reflect meaningful biological processes as well as relevant statistical uncertainty, both of which can yield valuable insights in evolutionary studies. We introduce a new tool for investigating phylogenetic incongruence through the exploration of phylogenetic tree landscapes. Our approach, implemented in the R package treespace , combines tree metrics and multivariate analysis to provide low‐dimensional representations of the topological variability in a set of trees, which can be used for identifying clusters of similar trees and group‐specific consensus phylogenies. treespace also provides a user‐friendly web interface for interactive data analysis and is integrated alongside existing standards for phylogenetics. It fills a gap in the current phylogenetics toolbox in R and will facilitate the investigation of phylogenetic results.     

The Revised Classification of Eukaryotes

This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re‐introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under‐sampled areas and from environmental genomic information.     

A Java applet for visualizing protein-protein interaction.

A web applet for browsing protein-protein interactions was implemented. It enables the display of interaction relationships, based upon neighboring distance and biological function. AVAILABILITY: The Java applet is available at http://www.charite.de/bioinformatics     

Generalized Venn diagrams: a new method of visualizing complex genetic set relations

MOTIVATION: Microarray experiments generate vast amounts of data. The unknown or only partially known functional context of differentially expressed genes may be assessed by querying the Gene Ontology database via GOMiner. Resulting tree representations are difficult to interpret and are not suited for visualization of this type of data. Methods are needed to effectively visualize these complex set relationships. RESULTS: We present a visualization approach for set relationships based on Venn diagrams. The proposed extension enhances the usual notion of Venn diagrams by incorporating set size information. The cardinality of the sets and intersection sets is represented by their corresponding circle (polygon) sizes. To avoid local minima, solutions to this problem are sought by evolutionary optimization. This generalized Venn diagram approach has been implemented as an interactive Java application (VennMaster) specifically designed for use with GOMiner in the context of the Gene Ontology database. AVAILABILITY: VennMaster is platform-independent (Java 1.4.2) and has been tested on Windows (XP, 2000), Mac OS X, and Linux. Supplementary information and the software (free for non-commercial use) are available at http://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestler/vennm together with a user documentation. CONTACT: hans.kestler@medizin.uni-ulm.de.     

现生长臂猿的新系统

本文综合形态、行为、生态、分布、染色体及有关化石资料的比较分析研究, 论述了白颊长臂猿(Hylobates leucog eny s) 和红颊长臂猿(Hylobates gabriellae) 的种级地位有效性; 着重讨论了黑长臂猿(Hylobates concolor) 及白眉长臂猿(Hylobates hoolock ) 的系统地位; 重新构建了现生11 种长臂猿系统发育的新系谱和依罗伯逊融合(Robert-sonian centric fusion) 进化途径的长臂猿演化假说。     

An enhanced Java graph applet interface for visualizing interactomes

SUMMARY: We have developed several new navigation features for a Java graph applet previously released for visualizing protein-protein interactions. This graph viewer can be used to navigate any molecular interactome dataset. We have successfully implemented this tool for exploring protein networks stored in the Bioverse interaction database. AVAILABILITY: http://bioverse.compbio.washington.edu/viewer CONTACT: ram@compbio.washington.edu.     

Java Treeview--extensible visualization of microarray data

Open source software encourages innovation by allowing users to extend the functionality of existing applications. Treeview is a popular application for the visualization of microarray data, but is closed-source and platform-specific, which limits both its current utility and suitability as a platform for further development. Java Treeview is an open-source, cross-platform rewrite that handles very large datasets well, and supports extensions to the file format that allow the results of additional analysis to be visualized and compared. The combination of a general file format and open source makes Java Treeview an attractive choice for solving a class of visualization problems. An applet version is also available that can be used on any website with no special server-side setup.     

The use of amplified fragment length polymorphism in determining species trees at fine taxonomic levels: analysis of a medically important snake, Trimeresurus albolabris

There are a huge number of phylogenetic studies based on mitochondrial DNA (mtDNA); however, these may represent gene trees that may not be congruent with the species tree. A solution to this problem is to include additional, independent, loci from the nuclear genome. At fine taxonomic levels, i.e. between populations and closely related species, previously suggested nuclear markers such as intron sequence data may not be appropriate. In this study we investigate the use of amplified fragment length polymorphisms (AFLP) to aid determination of the species tree for 24 specimens of a medically important snake, Trimeresurus albolabris. This is of particular importance for many venomous snakes as venom often varies intraspecifically. Five different primer combinations produced 434 bands and were analysed by constructing a phylogenetic tree using neighbour joining and principal component analysis. Results were similar across all methods and found distinct groupings. The results were compared with mtDNA data and a reconciled tree was constructed in order to determine the species tree for T. albolabris. We found that T. albolabris (sensu lato) is not monophyletic. Specimens from the Indonesian islands (except West Java) form a distinct clade and we propose elevation to species level. A specimen from Nepal is also distinct and suggests that this population also deserves specific status. We suggest that AFLPs may prove a valuable aid in determining species trees as opposed to gene trees at fine taxonomic levels and this should facilitate the incorporation of molecular data into such activities as antivenom production and conservation management.     

Using multi-temporal tree inventory data in eucalypt forestry to benchmark global high-resolution canopy height models. A showcase in Mato Grosso,Brazil

The global monitoring of forest structure worldwide is increasingly being supported by refined and enhanced satellite mission datasets. Forest canopy height is a global metric to characterise and monitor dynamics in forest ecosystems worldwide. Satellite mapping missions as NASA's Global Ecosystem Dynamics Investigation (GEDI) are creating opportunities to refine global forest canopy height models adding forest structural information to time-series satellite imagery. A recent global canopy height model presented by Lang et al., (2022) using GEDI and 10-m Sentinel-2 and the map from Potapov et al., (2020) using GEDI and Landsat are both tested in this study using multi-temporal tree-level data collected over eucalypt plantations in Brazil. Our results at plot-level showed Lang et al., (2022)’s estimates of canopy height came short compared to 2020 maximum and mean tree height records in the plots, 7.6 and 3.6 m, respectively, but adding CHM standard deviation improves the agreement of ground records for maximum tree height. Higher errors were computed for the plots in 2019 using the Potapov's 30-m CHM: 14.2 and 9.5 m, respectively. Averaged stand values were more similar between the three sources tested. We report improvement from the 30-m CHM to the 10-m, but still height saturation problems were observed when accounting for height differences in tall eucalypt trees. As more global products for forest height and biomass are becoming available to users, more validation exercises as presented in this study are needed to assess the suitability of CHM products to forestry needs, and facilitate the uptake and actionability of the next generation of global height and biomass products. We provide recommendations and insights on the use of GEDI laser data for global mapping and on the potential of commercial forestry areas to benchmark the accuracy of satellite mapping missions focusing on tree height estimation in the tropics.     

LVTree Viewer:An Interactive Display for the All-Species Living Tree Incorporating Automatic Comparison with Prokaryotic Systematics

We describe an interactive viewer for the All-Species Living Tree (LVTree). The viewer incorporates treeing and lineage information from the ARB-SILVA website. It allows collapsing the tree branches at different taxonomic ranks and expanding the collapsed branches as well, keeping the overall topology of the tree unchanged. It also enables the user to observe the consequence of trial lineage modifications by re-collapsing the tree. The system reports taxon statistics at all ranks automatically after each collapsing and re-collapsing. These features greatly facilitate the compar-ison of the 16S rRNA sequence phylogeny with prokaryotic taxonomy in a taxon by taxon manner. In view of the fact that the present prokaryotic systematics is largely based on 16S rRNA sequence analysis, the current viewer may help reveal discrepancies between phylogeny and taxonomy. As an application, we show that in the latest release of LVTree, based on 11,939 rRNA sequences, as few as 24 lineage modifications are enough to bring all but two phyla (Proteobacteria and Firmicutes) to monophyletic clusters.     

RNAmute: RNA secondary structure mutation analysis tool

Background  

RNAMute is an interactive Java application that calculates the secondary structure of all single point mutations, given an RNA sequence, and organizes them into categories according to their similarity with respect to the wild type predicted structure. The secondary structure predictions are performed using the Vienna RNA package. Several alternatives are used for the categorization of single point mutations: Vienna's RNAdistance based on dot-bracket representation, as well as tree edit distance and second eigenvalue of the Laplacian matrix based on Shapiro's coarse grain tree graph representation.