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MEGA Molecular Evolutionary Genetic Analysis, version 1.0. The Pennsylvania (1993)

by S Kumar, K Tamura, M Nei
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MEGA5: Molecular evolutionary genetics analysis using maximum . . .

by Koichiro Tamura, Daniel Peterson, Nicholas Peterson, Glen Stecher, Masatoshi Nei, Sudhir Kumar , 2011
"... 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 and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version ..."
Abstract - Cited by 7284 (25 self) - Add to MetaCart
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 and species. 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 trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. 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
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... hypotheses, estimating sequence divergences, web-based acquisition of sequence data, and expert systems to generate natural language descriptions of the analysis methods and data chosen by the user (=-=Kumar et al. 1994-=-, 2008; Kumar and Dudley 2007). With the fifth major release, the collection of analysis tools in MEGA has now broadened to include the maximum likelihood (ML) methods for molecular evolutionary analy...

Phylogenetic analysis by maximum likelihood (PAML). Version 1.1.

by Z YANG , 1995
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Abstract - Cited by 115 (2 self) - Add to MetaCart
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Theory of Correspondences

by Jessica A. Thompson, Mei Liu, Sophie Helaine, David W. Holden, David W. Holden, Sophie Helaine , 1984
"... Contribution of the PhoP/Q regulon to survival and ..."
Abstract - Cited by 84 (0 self) - Add to MetaCart
Contribution of the PhoP/Q regulon to survival and
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...omputer Group, Madison, WI, USA) (Womble, 2000). The sequence data were exported and further analysed using the Molecular Evolutionary Genetics Analysis (MEGA) software package versions 1.02 and 2.0 (=-=Kumar et al., 1994-=-). The relationships among the alleles, generated from pairwise allele comparisons using Hamming distance matrices (equivalent to p-distances), were visualized by split decomposition (Bandelt & Dress,...

Maximum likelihood of evolutionary trees: hardness and approximation

by Benny Chor, Tamir Tuller , 2005
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Abstract - Cited by 64 (5 self) - Add to MetaCart
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Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny,”Molecular Biology and Evolution,

by Claudia A M Russo , Naoko Takezaki , Masatoshi Nei , 1996
"... The relative efficiencies of different protein-coding genes of the mitochondrial genome and different tree-building methods in recovering a known vertebrate phylogeny (two whale species, cow, rat, mouse, opossum, chicken, frog, and three bony fish species) was evaluated. The tree-building methods e ..."
Abstract - Cited by 52 (2 self) - Add to MetaCart
The relative efficiencies of different protein-coding genes of the mitochondrial genome and different tree-building methods in recovering a known vertebrate phylogeny (two whale species, cow, rat, mouse, opossum, chicken, frog, and three bony fish species) was evaluated. The tree-building methods examined were the neighbor joining (NJ), minimum evolution (ME), maximum parsimony (MP), and maximum likelihood (ML), and both nucleotide sequences and deduced amino acid sequences were analyzed. Generally speaking, amino acid sequences were better than nucleotide sequences in obtaining the true tree (topology) or trees close to the true tree. However, when only first and second codon positions data were used, nucleotide sequences produced reasonably good trees. Among the 13 genes examined, Nd5 produced the true tree in all tree-building methods or algorithms for both amino acid and nucleotide sequence data. Genes Cytb and Nd4 also produced the correct tree in most tree-building algorithms when amino acid sequence data were used. By contrast, Co2, ZVdl, and Nd4Z showed a poor performance. In general, large genes produced better results, and when the entire set of genes was used, all tree-building methods generated the true tree. In each tree-building method, several distance measures or algorithms were used, but all these distance measures or algorithms produced essentially the same results. The ME method, in which many different topologies are examined, was no better than the NJ method, which generates a single final tree. Similarly, an ML method, in which many topologies are examined, was no better than the ML star decomposition algorithm that generates a single final tree. In ML the best substitution model chosen by using the Akaike information criterion produced no better results than simpler substitution models. These results question the utility of the currently used optimization principles in phylogenetic construction. Relatively simple methods such as the NJ and ML star decomposition algorithms seem to produce as good results as those obtained by more sophisticated methods. The efficiencies of the NJ, ME, MP and ML methods in obtaining the correct tree were nearly the same when amino acid sequence data were used. The most important factor in constructing reliable phylogenetic trees seems to be the number of amino acids or nucleotides used.

Genotype H: a new Amerindian genotype of hepatitis B virus revealed in Central

by Patricia Arauz-ruiz, Helene Norder, Betty H. Robertson, Lars O. Magnius , 2002
"... The complete genomes were sequenced for ten hepatitis B virus (HBV) strains. Two of them, from Spain and Sweden, were most similar to genotype D, although encoding d specificity. Five of them were from Central America and belonged to genotype F. Two strains from Nicaragua and one from Los Angeles, U ..."
Abstract - Cited by 45 (0 self) - Add to MetaCart
The complete genomes were sequenced for ten hepatitis B virus (HBV) strains. Two of them, from Spain and Sweden, were most similar to genotype D, although encoding d specificity. Five of them were from Central America and belonged to genotype F. Two strains from Nicaragua and one from Los Angeles, USA, showed divergences of 3�1–4�1 % within the small S gene from genotype F strains and were recognized previously as a divergent clade within genotype F. The complete genomes of the two genotype D strains were found to differ from published genotype D strains by
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... seqboot and consensus trees were generated by consense in the phylip package. The obtained trees were visualized with the tree drawing software treeview (Page, 1996). The mega program, version 1.02 (=-=Kumar et al., 1994-=-), was used to calculate nucleotide differences between the sequences. Results Complete genomes The genomes of strains 1853Nic, 1889Nic, 2928Nic, 1116Sal, 70H, 7768H and LAS2523 were 3215 nt long, as ...

A genomic timescale for the origin of eukaryotes

by S Blair Hedges, Hsiong Chen, Sudhir Kumar, Daniel Y-c Wang, A S Thompson, Hidemi Watanabe - BMC Evol. Biol , 2001
"... © 2001 Hedges et al; licensee BioMed Central Ltd. Verbatim copying and redistribution of this article are permitted in any medium for any non-commercial purpose, provided this notice is preserved along with the article's original URL. For commercial use, contact info@biomedcentral.com Backgroun ..."
Abstract - Cited by 38 (2 self) - Add to MetaCart
© 2001 Hedges et al; licensee BioMed Central Ltd. Verbatim copying and redistribution of this article are permitted in any medium for any non-commercial purpose, provided this notice is preserved along with the article's original URL. For commercial use, contact info@biomedcentral.com Background: Genomic sequence analyses have shown that horizontal gene transfer occurred during the origin of eukaryotes as a consequence of symbiosis. However, details of the timing and number of symbiotic events are unclear. A timescale for the early evolution of eukaryotes would help to better understand the relationship between these biological events and changes in Earth's environment, such as the rise in oxygen. We used refined methods of sequence alignment, site selection, and time estimation to address these questions with protein sequences from complete genomes of prokaryotes and eukaryotes. Results: Eukaryotes were found to evolve faster than prokaryotes, with those eukaryotes derived from eubacteria evolving faster than those derived from archaebacteria. We found an early time of divergence (~4 billion years ago, Ga) for archaebacteria and the archaebacterial genes in eukaryotes. Our analyses support at least two horizontal gene transfer events in the origin of eukaryotes, at 2.7 Ga and 1.8 Ga. Time estimates for the origin of cyanobacteria (2.6 Ga) and the
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...A gamma distance was used for all trees, with α estimated from the entire data set [45]. An analysis involving combined protein alignments was performed with maximum likelihood [50], neighbor joining =-=[49,51]-=-, and maximum parsimony [51], using bootstrapping. Bootstrap consensus trees show branch-lengths estimated by ordinary least-squares method [51]. Bootstrap support ≥ 95% was considered significant. Ac...

C-mos, a nuclear marker useful for squamate phylogenetic analysis.

by Kathleen M Saint , Christopher C Austin , Stephen C Donnellan , Mark N Hutchinson - Mol. Phylogenet. Evol. , 1998
"... Phylogenetic reconstruction in molecular systematics has largely been achieved using mitochondrial gene sequences and less frequently sequences of nuclear ribosomal RNA genes. At present few other nuclear genes have been identified that could be used to test these phylogenies. C-mos, a single-copy ..."
Abstract - Cited by 37 (1 self) - Add to MetaCart
Phylogenetic reconstruction in molecular systematics has largely been achieved using mitochondrial gene sequences and less frequently sequences of nuclear ribosomal RNA genes. At present few other nuclear genes have been identified that could be used to test these phylogenies. C-mos, a single-copy nuclear oncogene, has been identified as a candidate nuclear marker. Data are presented on the usefulness of c-mos sequences in the phylogenetic analysis of squamate reptile families. We obtained partial sequences of cmos from 13 squamate reptile families and outgroup representatives from the orders Rhynchocephalia, Chelonia, and Crocodylia. Phylogenetic analysis reveals a high degree of phylogenetic information contained within the sequence for both the synonymous and nonsynonymous substitutions. Phylogenetic resolution was present at both the deepest and shallower divergences but relationships among the major squamate lineages were not resolved, possibly because rapid cladogenesis may have led to the diversification of these lineages.
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...one codon in length and of these, three were within the snake clade, families Boidae and Typhlopidae. All the deletions occurred within a 41-bp region (bp 727–768 of human c-mos sequence). Inclusion of the deletions in the phylogenetic analysis did not change the topology of the trees recovered. Figure 1 shows the relationship between Jukes–Cantor corrected genetic distance and the proportion of synonymous and nonsynonymous differences between taxa (Jukes and Cantor, 1969). The genetic distances and proportion of synonymous and nonsynonymous differences were calculated using the program MEGA (Kumar et al., 1993). Polynomial regression lines were not significantly different from straight lines, indicating that saturation of third positions has not occurred and that there is phylogenetic signal at all codon positions. The mean pair-wise comparisons for Jukes–Cantor corrected genetic distances (6SD) and the proportion of amino acid substitutions (6SD), respectively, are: interordinal (n 5 89), 0.34 6 0.05 and 0.26 6 0.04; interfamilial (n 5 282), 0.26 6 0.07 and 0.24 6 0.04; and intrafamilial (n 5 18), 0.08 6 0.04 and 0.10 6 0.04. Of the 237 variable sites, 117 are third codon positions and 120 are at f...

Tempo and mode of nucleotide substitutions in gag and env gene fragments in human immunodeficiency virus type 1 populations with a known transmission history.

by Thomas Leitner , Sudhir Kumar , Jan Albert - J Virol , 1997
"... The complex evolutionary process of human immunodeficiency virus type 1 (HIV-1) is marked by a high level of genetic variation. It has been shown that the HIV-1 genome is characterized by variable and more constant regions, unequal nucleotide frequencies, and preference for G-to-A substitutions. Ho ..."
Abstract - Cited by 37 (4 self) - Add to MetaCart
The complex evolutionary process of human immunodeficiency virus type 1 (HIV-1) is marked by a high level of genetic variation. It has been shown that the HIV-1 genome is characterized by variable and more constant regions, unequal nucleotide frequencies, and preference for G-to-A substitutions. However, this knowledge has largely been neglected in phylogenetic analyses of HIV-1 nucleotide sequences, even though these analyses are applied to a number of important biological questions. The purpose of this study was to identify a realistic model of HIV-1 evolution and to statistically test if the application of such a model significantly improves the accuracy of phylogenetic analyses. A unique and recently reported HIV-1 transmission cluster consisting of nine infected individuals, for whom the direction and time for each transmission were exactly known, formed the basis for the analyses which were performed under a general model of nucleotide substitution using population sequences from the env V3 and p17 gag regions of the HIV-1 genome. Examination of seven different substitution models by maximum-likelihood methods revealed that the fit of the general reversible (REV) model was significantly better than that of simpler models, indicating that it is important to account for the asymmetric substitution pattern of HIV-1 and that the nucleotide substitution rate varied significantly across sites. The shape parameter ␣, which describes the variation across sites by a gamma distribution, was estimated to be 0.38 and 0.25 for env V3 and p17 gag , respectively. In env V3, the estimated average transition/ transversion rate ratio was 1.42. Thus, the REV model with variable rates across sites (described by a gamma distribution) provides the best description of HIV-1 evolution, whereas simple models are unrealistic and inaccurate. It is likely that the accuracy of phylogenetic studies of HIV-1 and many other viruses would improve substantially by the use of more realistic nucleotide substitution models. This is especially true when attempts are made to estimate the age of distant viral ancestors from contemporary viral sequences.
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...e parameter (�) of the gamma distribution estimated to be 0.38 and 0.25 for env V3 and p17 gag , respectively, can be used in, for instance, programs DNADIST in PHYLIP (under the Jin-Nei model), MEGA =-=(21)-=-, and the new PAUP*. These programs, and many others including the widely used maximum-likelihood program DNAML, can also be given a transition/transversion rate ratio. When there is no transition/ tr...

Sequence diversity of Pseudomonas aeruginosa: impact on population structure and genome evolution

by Claudia Kiewitz, Burkhard Tümmler, Claudia Kiewitz, Burkhard Tümmler, Medizinische Hochschule Hannover - J Bacteriol , 2000
"... These include: This article cites 48 articles, 29 of which can be accessed free at: ..."
Abstract - Cited by 36 (4 self) - Add to MetaCart
These include: This article cites 48 articles, 29 of which can be accessed free at:
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...ch partition for spatial clustering. Significant clustering of partition-specific sites indicates intragenic recombination. Phylogenetic analysis was performed using the PC program MEGA, Version 1.01 =-=(23)-=-. The numbers of synonymous nucleotide substitutions per 100 synonymous sites (d S) and nonsynonymous substitutions per 100 nonsynonymous sites (d N) were obtained by applying the Jukes-Cantor formula...

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