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...Continue Reading
Nonrandom amino acid substitution and estimation of the number of nucleotide substitutions in evolution
A method for estimating the number of invariant amino acid coding positions in a gene using cytochrome c as a model case
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0
Fast and slow implementations of relaxed-clock methods show similar patterns of accuracy in estimating divergence times.
Muscodor albus MOW12 an Endophyte of Piper nigrum L. (Piperaceae) Collected from North East India Produces Volatile Antimicrobials
Parvularcula oceani [corrected] sp. nov., isolated from deep-sea water of the Southeastern Pacific Ocean
Genetic structure and different color morphotypes suggest the occurrence and bathymetric segregation of two incipient species of Sebastes off Argentina
A transposable element insertion within ZmGE2 gene is associated with increase in embryo to endosperm ratio in maize.
Structure, transcription and post-transcriptional regulation of the bread wheat orthologs of the barley cleistogamy gene Cly1
Molecular characterisation of the amino- and carboxyl-domains in different Glu-A1x alleles of Triticum urartu Thum. ex Gandil
PCR and sequence analysis of barley chromosome 2H subjected to the gametocidal action of chromosome 2C
Molecular characterization of Als1, an acetohydroxyacid synthase mutation conferring resistance to sulfonylurea herbicides in soybean
Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC).
Thiofractor thiocaminus gen. nov., sp. nov., a novel hydrogen-oxidizing, sulfur-reducing epsilonproteobacterium isolated from a deep-sea hydrothermal vent chimney in the Nikko Seamount field of the northern Mariana Arc
Genome analysis and heterologous expression of acetate-activating enzymes in the anammox bacterium Kuenenia stuttgartiensis.
Paenibacillus profundus sp. nov., a deep sediment bacterium that produces isocoumarin and peptide antibiotics
Themoanaerobacterium calidifontis sp. nov., a novel anaerobic, thermophilic, ethanol-producing bacterium from hot springs in China.
Metabolic regulation and chromosomal localization of carbaryl degradation pathway in Pseudomonas sp. strains C4, C5 and C6
The diversity of Rhizobia, Sinorhizobia and novel non-Rhizobial Paenibacillus nodulating wild herbaceous legumes
Identification of a possible respiratory arsenate reductase in Denitrovibrio acetiphilus, a member of the phylum Deferribacteres
Location and contribution of individual β-glucosidase from Neurospora crassa to total β-glucosidase activity
Avian coronavirus spike glycoprotein ectodomain shows a low codon adaptation to Gallus gallus with virus-exclusive codons in strategic amino acids positions.
Extreme conservation of the psaA/psaB intercistronic spacer reveals a translational motif coincident with the evolution of land plants
Molecular evolution of translin superfamily proteins within the genomes of eubacteria, archaea and eukaryotes
Evolutionary analysis and lateral gene transfer of two-component regulatory systems associated with heavy-metal tolerance in bacteria
Evolution of the ABPA subunit of androgen-binding protein expressed in the submaxillary glands in New and Old World rodent taxa
Characteristics of MHC class I genes in house sparrows Passer domesticus as revealed by long cDNA transcripts and amplicon sequencing
pAO1 of Arthrobacter nicotinovorans and the spread of catabolic traits by horizontal gene transfer in gram-positive soil bacteria
Evolution of plant mitochondrial intron-encoded maturases: frequent lineage-specific loss and recurrent intracellular transfer to the nucleus
Characterization of antibiotic-resistance genes in antibiotic resistance Escherichia coli isolates from a lake
Geographic specific coral-associated ammonia-oxidizing archaea in the northern Gulf of Eilat (Red Sea).
Bioinformatics in Biomedicine
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