title: jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences.
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.
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University Shilim-dong, Kwanak-gu, Seoul, Republic of Korea.
authors.forename: Yoon-Seong
authors.initials: YS
authors.lastname: Jeon
authors.forename: Hwanwon
authors.initials: H
authors.lastname: Chung
authors.forename: Sunyoung
authors.initials: S
authors.lastname: Park
authors.forename: Inae
authors.initials: I
authors.lastname: Hur
authors.forename: Jae-Hak
authors.initials: JH
authors.lastname: Lee
authors.forename: Jongsik
authors.initials: J
authors.lastname: Chun
mesh_terms: D000465:Algorithms; D019143:Evolution, Molecular; D010802:Phylogeny; D011381:Programming Languages; D012335:RNA, Ribosomal / Q000032:analysis / Q000737:chemistry* / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D018511:Systems Integration; D014584:User-Computer Interface
chemical_list: D012335:RNA, Ribosomal