A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2008; you can also visit the original URL.
The file type is application/pdf.
Filters
MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences
2008
Briefings in Bioinformatics
Preserved Fulltext
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
2007
Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2021
Zenodo
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
Preserved Fulltext
The Internet Archive has digitized a microfilm copy of this work. It may be possible to borrow a copy for reading.
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
2011
Molecular biology and evolution
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2010
Limnology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2009
Current Genomics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2010; you can also visit the original URL.
The file type is application/pdf.
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
2017
Journal of Biotechnology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2020
PLoS ONE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2013
Briefings in Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2010
Limnology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2010
Microbial Ecology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
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
2019
PLoS ONE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2018
PLoS ONE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 71 results