<name>C</name> </clade> </clade> </phylogeny> </phyloxml> Han, Mira V.; Zmasek, Christian M. (2009). "phyloXML: XML for evolutionary biology and comparative...
4 KB (352 words) - 05:17, 19 May 2025
TREES; Tree tree1 = ((Alpha,Beta),Gamma,Delta); END; Newick format NeXML format phyloXML Maddison DR, Swofford DL, Maddison WP (1997). "NEXUS: An extensible...
5 KB (323 words) - 22:56, 26 January 2025
the phylogenetic network software PhyloNet makes use of both the Extended Newick and Rich Newick format. phyloXML T-REX (Webserver) allows handling phylogenetic...
14 KB (1,663 words) - 05:17, 2 April 2025
formats are supported for reading and writing, including Newick, NEXUS and phyloXML. Common tree manipulations and traversals are supported via the Tree and...
19 KB (2,024 words) - 13:38, 21 July 2025
Bel M (September 2017). "PhyD3: a phylogenetic tree viewer with extended phyloXML support for functional genomics data visualization". Bioinformatics. 33...
24 KB (1,650 words) - 12:26, 24 June 2025
the phyloXML format. Archaeopteryx is the successor to Java program A Tree Viewer (ATV). Han, Mira V.; Zmasek, Christian M. (2009). "phyloXML: XML for...
2 KB (140 words) - 04:13, 2 December 2023
complement MathML. OPML: an XML format for outlines phyloXML – XML for phylogenetic and phylogenomic applications PMML – XML for predictive analytics and...
22 KB (2,634 words) - 08:54, 10 July 2025
BEAST 2 (section LinguaPhylo)
can be installed via BEAUti out of the box. A related project is LinguaPhylo (LPhy). LPhy is a probabilistic programming language for defining phylogenetic...
5 KB (589 words) - 05:43, 9 February 2025
D.; Scornavacca, C.; Szöllosi, G.; Zhang, L.; Daubin, V. (2018). "RecPhyloXML: A format for reconciled gene trees". Bioinformatics. 34 (21): 3646–3652...
141 KB (15,304 words) - 11:59, 22 May 2025
packages biojava-core, biojava-structure, biojava-structure-gui, biojava-phylo, as well as others. BioJava 4.2.0 was the first release to be available...
33 KB (4,099 words) - 10:35, 19 March 2025