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

Young-Sang Jeon | Zendy; HeeChun Chung | Zendy; Sung Sup Park | Zendy; Inae Hur | Zendy; Jehee Lee | Zendy; Jongsik Chun | Zendy

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

Author(s) -

Young-Sang Jeon,

HeeChun Chung,

Sung Sup Park,

Inae Hur,

Jehee Lee,

Jongsik Chun

Publication year - 2005

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bti463

Subject(s) - phylogenetic tree , phylogenetics , ribosomal rna , biology , computational biology , pairwise comparison , java , 28s ribosomal rna , rna , genetics , computer science , ribosome , programming language , gene , artificial intelligence

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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