Projects

nexml

XML-based data exchange standard for phylogenetics. In honor of the commonly-used "nexus" flat file format, the working title for this standard is nexml.

Bio::Phylo

Phylogenetic analysis using perl.

Cipres-perl

Perl stack for the Cyber-Infrastructure for Phylogenetic Research (CIPRES)

phyloXML

phyloXML is an XML language for the analysis, exchange, and storage of phylogenetic trees (or networks) and associated data. The structure of phyloXML is described by XML Schema Definition (XSD) language. A shortcoming of current formats for describing phylogenetic trees (such as Nexus and ... [More] Newick/New Hampshire) is a lack of a standardized means to annotate tree nodes and branches with distinct data fields (which in the case of a basic species tree might be: taxon names, branch lengths, and, possibly multiple, support values). Data storage and exchange is even more cumbersome in studies in which trees are the result of a reconciliation of some kind. [Less]

ATV

ATV is a Java tool for the visualization of annotated phylogenetic trees. It can be used both as applets (ATVe, ATVapplet) and as a standalone application.