jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences.
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.
Jeon
Yoon-Seong
YS
Interdisciplinary Program in Bioinformatics, Seoul National University Shilim-dong, Kwanak-gu, Seoul, Republic of Korea.
Chung
Hwanwon
H
Park
Sunyoung
S
Hur
Inae
I
Lee
Jae-Hak
JH
Chun
Jongsik
J
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
D012335:RNA, Ribosomal