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jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences.

Yoon-Seong Jeon·Hwanwon Chung·Sunyoung Park·Inae Hur·Jae-Hak Lee·Jongsik Chun
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Abstract

jPHYDIT is a Java application designed to furnish a visual and integrated environment for molecular phylogeny. The program can be used to visualize intra-strand base-pairing information in secondary and tertiary structures of ribosomal RNA (rRNA) sequences. A function for the semi-automated alignment was included to facilitate handling of the database containing a large number of multiple-aligned rRNA sequences. Integration of nucleotide sequence editing, pairwise alignment, multiple alignment and phylogenetic treeing functions provide an easy and efficient way of analyzing rRNA sequences for molecular evolution, systematics, epidemiology and ecology.

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AlgorithmsEvolution, MolecularPhylogenyProgramming LanguagesRNA, RibosomalSequence AlignmentSequence Analysis, RNASequence Homology, Nucleic AcidSoftwareSystems IntegrationUser-Computer InterfaceJournal ArticleResearch Support, Non-U.S. Gov't

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Yoon-Seong Jeon, Hwanwon Chung, Sunyoung Park, Inae Hur, Jae-Hak Lee, Jongsik Chun. 2005-04-26. jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences.. https://doi.org/10.1093/bioinformatics%2Fbti463

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