Abstract
BackgroundEvolutionary analysis provides a formal framework for comparative analysis of genomic and other data. In evolutionary analysis, observed data are treated as the terminal states of characters that have evolved (via transitions between states) along the branches of a tree. The NEXUS standard of Maddison, et al. (1997; Syst. Biol. 46: 590–621) provides a portable, expressive and flexible text format for representing character-state data and trees. However, due to its complexity, NEXUS is not well supported by software and is not easily accessible to bioinformatics users and developers.ResultsBio::NEXUS is an application programming interface (API) implemented in Perl, available from CPAN and SourceForge. The 22 Bio::NEXUS modules define 351 methods in 4229 lines of code, with 2706 lines of POD (Plain Old Documentation). Bio::NEXUS provides an object-oriented interface to reading, writing and manipulating the contents of NEXUS files. It closely follows the extensive explanation of the NEXUS format provided by Maddison et al., supplemented with a few extensions such as support for the NHX (New Hampshire Extended) tree format.ConclusionIn spite of some limitations owing to the complexity of NEXUS files and the lack of a formal grammar, NEXUS will continue to be useful for years to come. Bio::NEXUS provides a user-friendly API for NEXUS supplemented with an extensive set of methods for manipulations such as re-rooting trees and selecting subsets of data. Bio::NEXUS can be used as glue code for connecting existing software that uses NEXUS, or as a framework for new applications.
Highlights
Evolutionary analysis provides a formal framework for comparative analysis of genomic and other data
Structure of Bio::NEXUS objects The structure of Bio::NEXUS objects reflects the organization of the NEXUS file format, as well as the implicit data models used in bioinformatics
Datasets can contain multiple trees, in which case this procedure would affect the default tree, unless a different tree is specified by name
Summary
Examples of utility code: re-naming, re-rooting, and format conversion Bio::NEXUS facilitates rapid development of utility scripts and "glue code" for typical bioinformatics tasks such as creating formatted files, manipulating data in files, converting formats, and developing wrappers. $nexus_obj->write('renamed.nex'); BEGIN TREES; TREE my_tree = (((A:2,B:3):1,C:1):1,D:1)root; In the course of carrying out a scientific analysis, researchers will often wish to carry out complex operations that edit, transform or otherwise manipulate data stored in a file While such steps often can be done "by hand" using a text editor, software tools reduce errors and allow automation. My $nexus_obj = new Bio::NEXUS('example.nex'); $nexus_obj = $nexus_obj->reroot('A'); $nexus_obj->write('rerooted.nex'); In the example below of converting to the format used by the PHYLIP [14] package, an additional line of code is required to get and print the number of taxa (OTUs) along with the length of the alignment (using get_ntax and get_nchar). As the NEXUS standard allows taxa to be referenced by a number representing the order in which they were declared, the data for an OTU are not always associated creates an output file "outfile" with only columns (characters) 1–3, 8, and 10–45 selected from the input file "infile". The server responds by generating an image of the data and by mapping such things as JavaScript pop-up menus to the nodes of tree that allow the user to re-root a tree, exclude or select a subtree, and so on
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