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MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences

S. Kumar, M. Nei, J. Dudley, K. Tamura
2008 Briefings in Bioinformatics  
with a special emphasis on inferring evolutionary relationships and patterns of DNA and protein evolution.  ...  The Molecular Evolutionary Genetics Analysis (MEGA) software is a desktop application designed for comparative analysis of homologous gene sequences either from multigene families or from different species  ...  Acknowledgements Support for this work comes, in part, from the National Institutes of Health (S.K., M.N.) and Japan Society of Promotion of Science (K.T., S.K.).  ... 
doi:10.1093/bib/bbn017 pmid:18417537 pmcid:PMC2562624 fatcat:ug2zvtln7bet7mz2jjsdv22ml4

Bioinformatics software for biologists in the genomics era

S. Kumar, J. Dudley
2007 Bioinformatics  
often employed for the analysis of large numbers of genes, long genomic segments and groups of sequences.  ...  Coupled with fast-declining, per-base sequencing costs, this influx of DNA sequence data has encouraged laboratory scientists to engage large datasets in comparative sequence analyses for making evolutionary  ...  used to generate citation impact for various software S.  ... 
doi:10.1093/bioinformatics/btm239 pmid:17485425 fatcat:vuehtzvqnfdchewedsnqfvzotu

Upshot of Percentage Consistency and the Sum-of-Pairs Score Factor on the Algorithmic Structures of some DNA Analysis Tools

F. U. Ogban, E. A. Edim, E. E. Essien, O. A. Ofem, E. B. Edim
2021 Zenodo  
One of the most popular quantitative measurements for multiple sequence alignment (MSA) is the Sum-of-Pair score, or simply sum-of-pair (SP).  ...  Keywords: Sum-of-pairs score, Percentage Consistency, Algorithmic approaches, DNA sequencing tools, Jalveiw, Sequencing methods,  ...  The MEGA software project grew out of the need for employing statistical methods in the phylogenetic analysis of DNA and protein sequences in the early 1990s.  ... 
doi:10.5281/zenodo.5504160 fatcat:sbs4fpjk7jdflmgmmpd3elcani

Page 128 of Genetics Vol. 183, Issue 5 [page]

2009 Genetics  
Ner and K. Tamura, 2008 MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief. Bioinformatics 9: 299-306. LAUGEL, V., C. DALLOz, A. STARY, V.  ...  BLAISDELL and S. KARLIN, 1992 Methods and algorithms for statistical analysis of protein sequences. Proc. Natl. Acad. Sci.USA 89: 2002- 2006. BurGE, C., and S.  ... 

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

K. Tamura, D. Peterson, N. Peterson, G. Stecher, M. Nei, S. Kumar
2011 Molecular biology and evolution  
Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic  ...  Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes  ...  The MEGA software project is supported by research grants from National Institutes of Health to S.K. and M.N.  ... 
doi:10.1093/molbev/msr121 pmid:21546353 pmcid:PMC3203626 fatcat:cbyso6eaxzczbdafyuxufwbyii

Rapid expansion of the distributional range and the population genetic structure of the freshwater amphipod Crangonyx floridanus in Japan

Asako Nagakubo, Kazuki Sekiné, Yoshiki Tanaka, Ryoichi B. Kuranishi, Shoji Kanada, Koji Tojo
2010 Limnology  
populations based on nuclear (18S rRNA) and mitochondrial (COI) DNA sequences.  ...  A limited number of individuals from a North American native population were probably inadvertently introduced and established somewhere within the Kanto region.  ...  Yoshida (NPO Research Office of Sustainable Riversystems for Natural Cultural Features), K. Miyazaki (Kyoto University) and K. Satake (Ntional Institute for Environmental Studies. We  ... 
doi:10.1007/s10201-010-0323-3 fatcat:kizgjt7pijhbpavsichqdsxykq

Signal Processing for Metagenomics: Extracting Information from the Soup

Gail Rosen, Bahrad Sokhansanj, Robi Polikar, Mary Bruns, Jacob Russell, Elaine Garbarine, Steve Essinger, Non Yok
2009 Current Genomics  
Although metagenomic studies have shed a great deal of insight into bacterial diversity and coding capacity, several computational challenges remain due to the massive size and complexity of metagenomic  ...  without the need for cultivation.  ...  Numerous researchers have developed software tools both to aid in the alignment of sequences and tools for developing phylogenetic (evolutionary) trees, all of which can be utilized for taxonomic purposes  ... 
doi:10.2174/138920209789208255 pmid:20436876 pmcid:PMC2808676 fatcat:lb67lmbuhzaxlpok6itzeift5y

25 years of serving the community with ribosomal RNA gene reference databases and tools

Frank Oliver Glöckner, Pelin Yilmaz, Christian Quast, Jan Gerken, Alan Beccati, Andreea Ciuprina, Gerrit Bruns, Pablo Yarza, Jörg Peplies, Ralf Westram, Wolfgang Ludwig
2017 Journal of Biotechnology  
At that time, the ARB project maintained both, the sequence reference datasets and the software package for data analysis.  ...  In 2005, with the massive increase of DNA sequence data, the maintenance of the software system ARB and the corresponding rRNA databases SILVA was split between Munich and the Microbial Genomics and Bioinformatics  ...  Your immediate critical evaluation is a great motivation for us to improve our databases and tools.  ... 
doi:10.1016/j.jbiotec.2017.06.1198 pmid:28648396 fatcat:u35qpimwazhhnip774tn433bha

Comparative analysis of plastid genomes within the Campanulaceae and phylogenetic implications

Chun-Jiao Li, Ruo-Nan Wang, De-Zhu Li
2020 PLoS ONE  
Almost all protein-coding genes and amino acid sequences showed obvious codon preferences.  ...  Hotpot regions were considered to be useful molecular markers for resolving phylogenetic relationships and species authentication of Campanulaceae.  ...  Acknowledgments We appreacite the assistance of Prof. Jun-Bo Yang (Kunming Institute of Botany, Chinese Academy of Sciences) during the experiments.  ... 
doi:10.1371/journal.pone.0233167 pmid:32407424 pmcid:PMC7224561 fatcat:x4d6mfmfjjgvbbgq3oqxxdemjm

Teaching the ABCs of bioinformatics: a brief introduction to the Applied Bioinformatics Course

J. Luo
2013 Briefings in Bioinformatics  
With the development of the Internet and the growth of online resources, bioinformatics training for wet-lab biologists became necessary as a part of their education.  ...  and the Chinese Academy of Agricultural Sciences for the past 13 years.  ...  Special thanks to Dr Lisa Mullan for her help in critical reading and language editing of the manuscript.  ... 
doi:10.1093/bib/bbt065 pmid:24008274 pmcid:PMC4239802 fatcat:6x7k5ib7ezccrkefqiv44mpf2e

Habitat segregation and genetic relationship of two heptageniid mayflies, Epeorus latifolium and Epeorus l-nigrus, in the Shinano-gawa River basin

Masaki Ogitani, Kazuki Sekiné, Koji Tojo
2010 Limnology  
analysis of nymphs and also some male adults of which it was able to reliably differentiate between the two species.  ...  Based on our genetic analysis, including several male adult specimens of E. latifolium and E. l-nigrus, it was clearly revealed that E. latifolium and E. l-nigrus are respectively form two separate monophyletic  ...  We express our thanks to the Chikuma River Office (Hokuriku Regional Development Bureau, Ministry of Land Infrastructure and Transport) and the Chikuma River Ecology Research Group, for their cooperation  ... 
doi:10.1007/s10201-010-0328-y fatcat:fojceqcsmzcrhkb5tzyko2jzgu

Fungal Community Analysis in the Deep-Sea Sediments of the Central Indian Basin by Culture-Independent Approach

Purnima Singh, Chandralata Raghukumar, Pankaj Verma, Yogesh Shouche
2010 Microbial Ecology  
Community DNA isolated from these sediments was amplified using universal and fungal-specific ITS and universal 18S rDNA primer pairs.  ...  The majority of the recovered sequences belonged to diverse phylotypes of Ascomycota and Basidiomycota. Our results suggested the existence of cosmopolitan marine fungi in the sediments of CIB.  ...  Acknowledgements The first author is thankful to University Grants Commission for the award of Senior Research Fellowship and Dr.  ... 
doi:10.1007/s00248-010-9765-8 pmid:21057784 fatcat:ve454aqqezeidg4vumyak2jxli

First complete chloroplast genomics and comparative phylogenetic analysis of Commiphora gileadensis and C. foliacea: Myrrh producing trees

Arif Khan, Sajjad Asaf, Abdul Latif Khan, Ahmed Al-Harrasi, Omar Al-Sudairy, Noor Mazin AbdulKareem, Adil Khan, Tariq Shehzad, Nadiya Alsaady, Ali Al-Lawati, Ahmed Al-Rawahi, Zabta Khan Shinwari (+1 others)
2019 PLoS ONE  
A modified chloroplast DNA extraction method was adopted, followed with next generation sequencing, detailed bioinformatics and PCR analyses.  ...  Herein, we report the complete chloroplast genome sequences of C. gileadensis and C. foliacea and comparative analysis with related species (C. wightii and Boswellia sacra).  ...  Kumar S, Nei M, Dudley J, Tamura K (2008) MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences.  ... 
doi:10.1371/journal.pone.0208511 pmid:30629590 pmcid:PMC6328178 fatcat:t2koy2mjejdbhninubckmchrkq

Molecular study of Mitochondrial MT-TL1Leucine gene and some Biochemical parameters in association with Coronary Heart Disease in patients attending Erbil cardiac center

2017 Zanco Journal of Pure and Applied Sciences  
The statistical analysis showed significant difference at the level of 0.05 between coronary atherosclerotic patients and normal healthy control in terms of the mean of diabetic (for females 169.200 ±  ...  The results of MT-TL1 Leucine UUR gene sequencing were clearly showed no polymorphic mutation to be linked with regards to the disease status or development with those published in the NCBI database, indicating  ...  MEGA: A biologist-centric softwarefor evolutionary analysis of DNA and protein sequences. Brief. Bioinf., 9: 299-306. LIM, J., CRESPO-BARRETO, J., JAFAR-NEJAD, P., BOWMAN, A.  ... 
doi:10.21271/zjpas.29.5.9 fatcat:z3a4ok7ksrbr7lupjcx646ta2a

Complete chloroplast genome sequence and comparative analysis of loblolly pine (Pinus taeda L.) with related species

Sajjad Asaf, Abdul Latif Khan, Muhammad Aaqil Khan, Raheem Shahzad, Lubna, Sang Mo Kang, Ahmed Al-Harrasi, Ahmed Al-Rawahi, In-Jung Lee, Hikmet Budak
2018 PLoS ONE  
Thus, the complete P. taeda genome provided valuable resources for population and evolutionary studies of gymnosperms and can be used to identify related species.  ...  SM, et al. (2018) Complete chloroplast genome sequence and comparative analysis of loblolly pine (Pinus taeda L.) with related species.  ...  MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform. 2008; 9(4):299-306.  ... 
doi:10.1371/journal.pone.0192966 pmid:29596414 pmcid:PMC5875761 fatcat:aocfrovywzhapmuvjvaph6g4gq
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