Archaeopteryx is an interactive computer software program, written in Java, for viewing, editing, and analyzing phylogenetic trees. This type of program can be used for a variety of analyses of molecular data sets, but is particularly designed for phylogenomics. Besides tree description formats with limited expressiveness (such as Newick/New Hamphshire, Nexus), it also implements the phyloXML format. Archaeopteryx is the successor to Java program A Tree Viewer (ATV).
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References
Han, Mira V.; Zmasek, Christian M. (2009). "phyloXML: XML for evolutionary biology and comparative genomics". BMC Bioinformatics. 10: 356. doi:10.1186/1471-2105-10-356. PMC 2774328. PMID 19860910. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774328 ↩
Zmasek, Christian M.; Eddy, Sean R. (2001). "ATV: display and manipulation of annotated phylogenetic trees". Bioinformatics. 17 (4): 383–384. doi:10.1093/bioinformatics/17.4.383. PMID 11301314. https://doi.org/10.1093%2Fbioinformatics%2F17.4.383 ↩