Bioinformatics

Bioinformatics Advance Access originally published online on April 26, 2005
Bioinformatics 2005 21(14):3171-3173; doi:10.1093/bioinformatics/bti463

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

Yoon-Seong Jeon ¹, Hwanwon Chung ¹, Sunyoung Park ², Inae Hur ¹, Jae-Hak Lee ¹ and Jongsik Chun ^1,2,*

¹Interdisciplinary Program in Bioinformatics, Seoul National University Shilim-dong, Kwanak-gu, Seoul, Republic of Korea
²School of Biological Sciences, Seoul National University Shilim-dong, Kwanak-gu, Seoul, Republic of Korea

^*To whom correspondence should be addressed.

Summary: 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.

Availability: jPHYDIT is available freely over the Internet at http://chunlab.snu.ac.kr/jphydit/. The platform-independent JAVA technology provides distributions for various operating systems and hardware architectures.

Contact: jchun{at}snu.ac.kr

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Received on December 9, 2004; revised on April 2, 2005; accepted on April 21, 2005

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