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), ATV also implements the phyloXML^[1] format. Archaeopteryx is the successor to the 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

Genomics	Cognitive genomics Computational genomics Comparative genomics Functional genomics Genome project Human Genome Project Metagenomics Personal genomics Social genomics Structural genomics

Bioinformatics	Biochip Cheminformatics Chemogenomics Connectomics Glycomics Immunomics Lipidomics Metabolomics Microbiomics Nutrigenomics Paleopolyploidy Pharmacogenetics Pharmacogenomics Systems biology Toxicogenomics Transcriptomics

Structural biology	Proteomics Human Proteome Project call-map proteomics structure-based drug design expression proteomics

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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