Affiliation: Tokyo Metropolitan University
- Evolutionary distance estimation under heterogeneous substitution pattern among lineagesKoichiro Tamura
Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
Mol Biol Evol 19:1727-36. 2002..We also discuss the relationship of the substitution and mutation rate estimates when the substitution pattern is not the same in the lineages leading to the two sequences compared...
- Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Unusual evolution of interspersed repeat sequences in the Drosophila ananassae subgroupMasafumi Nozawa
Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, Tokyo, Japan
Mol Biol Evol 23:981-7. 2006..Such an atypical combination of characteristics (i.e., wide dispersal and tandem repetition) may have been generated by these different transposition mechanisms during the course of evolution...
- A novel chimeric gene, siren, with retroposed promoter sequence in the Drosophila bipectinata complexMasafumi Nozawa
Department of Biological Sciences, Graduate School of Science, Tokyo Metropolitan University, 1 1 Minami Ohsawa, Hachioji shi, Tokyo 192 0397, Japan
Genetics 171:1719-27. 2005..The potential of retroposition to produce a copy of promoter and intron sequences in the context of gene overlapping was demonstrated...
- Estimating divergence times in large molecular phylogeniesKoichiro Tamura
Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192 0397, Japan
Proc Natl Acad Sci U S A 109:19333-8. 2012....
- MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysisSudhir Kumar
Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University ASU, Tempe, AZ 85287 5301, USA
Bioinformatics 28:2685-6. 2012..Here, we describe MEGA-CC and outline the steps for using MEGA-CC in tandem with MEGA-Proto for iterative and automated data analysis...
- MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methodsKoichiro Tamura
Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
Mol Biol Evol 28:2731-9. 2011..This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net...
- Replication origin of mitochondrial DNA in insectsShigeru Saito
Department of Biological Sciences, Tokyo Metropolitan University, Hachiouji, Tokyo 192 0397, Japan
Genetics 171:1695-705. 2005....
- Prospects for inferring very large phylogenies by using the neighbor-joining methodKoichiro Tamura
Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe, 85287 4501, USA
Proc Natl Acad Sci U S A 101:11030-5. 2004..Our results encourage the use of complex models of nucleotide substitution for estimating evolutionary distances and hint at bright prospects for the application of the NJ and related methods in inferring large phylogenies...
- Phylogeny of the Drosophila immigrans species group (Diptera: Drosophilidae) based on Adh and Gpdh sequencesToru Katoh
COE for Neo Science of Natural History, Graduate School of Science, Hokkaido University, North 10 West 8, Sapporo 060 0810, Japan
Zoolog Sci 24:913-21. 2007..maculinotata of the funebris group, although the phylogenetic relationships within this clade remain uncertain and need to be substantiated with further studies. Thus, according to the present study, the immigrans group is polyphyletic...
- MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequencesSudhir Kumar
Biodesign Institute, A240, Arizona State University, Tempe, AZ 85287 5301, USA
Brief Bioinform 9:299-306. 2008..We also discuss how MEGA might evolve in the future to assist researchers in their growing need to analyze large data set using new computational methods...
- Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocksKoichiro Tamura
Center for Evolutionary Functional Genomics, Arizona Biodesign Institute, and School of Life Sciences, Arizona State University, USA
Mol Biol Evol 21:36-44. 2004..The inferred temporal pattern of fruit fly evolution shows correspondence with the cooling patterns of paleoclimate changes and habitat fragmentation in the Cenozoic...
- MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignmentSudhir Kumar
Life Sciences A 351, The Biodesign Institute, Tempe, AZ 85287 4501, USA
Brief Bioinform 5:150-63. 2004..This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA...
- MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0Koichiro Tamura
Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, AZ, USA
Mol Biol Evol 24:1596-9. 2007..The current version of MEGA is available free of charge at (http://www.megasoftware.net)...