Archaeopteryx (evolutionary tree visualization and analysis)

Archaeopteryx
Developer(s)	Christian M. Zmasek

Stable release	0.972+ beta 9M / 2012.08.08
Operating system	Windows, Linux, Mac OS X
Type	Bioinformatics
License	LGPL
Website	https://sites.google.com/site/cmzmasek/home/software/archaeopteryx

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^[1] format. Archaeopteryx is the successor to Java program A Tree Viewer (ATV).^[2]

References

↑ Han, Mira V.; Zmasek, Christian M. (2009). "phyloXML: XML for evolutionary biology and comparative genomics". BMC Bioinformatics. United Kingdom: BioMed Central. 10: 356. doi:10.1186/1471-2105-10-356. PMC 2774328. PMID 19860910.
↑ Zmasek, Christian M.; Eddy, Sean R. (2001). "ATV: display and manipulation of annotated phylogenetic trees". Bioinformatics. United Kingdom: Oxford Journals. 17 (4): 383–384. doi:10.1093/bioinformatics/17.4.383. PMID 11301314.

External links

Omics

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Research tools	2-D electrophoresis Mass spectrometer Electrospray ionization Matrix-assisted laser desorption ionization Matrix-assisted laser desorption ionization-time of flight mass spectrometer Spotted array-based tools Microfluidic-based tools Isotope affinity tags Molecular scanner

Organizations	National Institutes of Health (USA) DNA Data Bank of Japan (JP) European Molecular Biology Laboratory (EU) Sanger Centre (EN)

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