About jPHYDIT

jPHYDIT stands for "Phylogenetic Editor for JAVA". The program is a molecular sequence editor specially designed for phylogenetic analysis such as ribosomal RNA sequences. It is the successor of MS Windows-based PHYDIT program. PHYDIT will be no longer supported or developed as we have switched our main project to java-based jPHYDIT.

Current version of jPHYDIT is 1.0

jPHYDIT displays secondary/tertiary structure pairings of ribosomal RNA molecules whiling users edit nucleotide sequences. This process allows users to do "alignment based on rRNA secondary structure" which is required for the precise phylogenetic inference (See Hickson et al. 1996; Ludwig & Schleifer, 1994).

Acknowledgement

jPHYDIT project has been supported by a grant of International Mobile Telecommunications 2000 R&D Project, Ministry of Information & Communication, Republic of Korea.

Paper on jPHYDIT

jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences. BIOINFORMATICS, vol.12 no.142005, pages 3171-3173

References

Hickson, R. E., C. Simon, A. Cooper, G. S. Spicer, J. Sullivan, and D. Penny. 1996. Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA. Mol Biol Evol 13: 150-169.
Ludwig W, Schleifer KH. 1994. Bacterial phylogeny based on 16S and 23S rRNA sequence analysis. FEMS Microbiol Rev. 15(2-3):155-73