[PDF] MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. | Semantic Scholar (2024)

New additions are described that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods and a Bayesian method for estimating neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments.

New additions are described that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed ‐ clock methods and a Bayesian method for estimating neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments.

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine and has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses.

A simple and fast protocol for data preparation and high quality phylogenetic tree inferences using simple to install cross-platform software applications with rich graphical interfaces to provide insight into the evolution of GULO gene in animals.

The macOS version of the MEGA software, which eliminates the need for virtualization and emulation programs, has a native Cocoa graphical user interface that is programmed to provide a consistent user experience across macOS, Windows, and Linux.

New functions include imputing missing distances and phylogeny simultaneously simultaneously, new bootstrapping/jackknifing methods for PhyPA, and an improved function for fast and accurate estimation of the shape parameter of the gamma distribution for fitting rate heterogeneity over sites.

This paper shows how the sequence data file used for the phylogenetic analyses can now be obtained much faster by changing the way coding sequence isoforms are removed, using the newly implemented SEDA operation “Remove isoforms”.

A user-friendly software that uses genome-wide SNPs to construct and display phylogenetic trees in seconds to minutes and produces pairwise-diversity matrix in MEGA and PHYLIP file formats as well as trees in the Newick format which could be directly used by other popular phylogenetic software programs.

A one-click user-friendly software that uses gnome-wide SNPs to construct and display phylogenetic trees in seconds to minutes and produces pairwise-diversity matrix in MEGA and PHYLIP file formats which could be directly used by other phylogenetic software programs.

PhyloSuite is a user-friendly workflow desktop platform dedicated to streamlining molecular sequence data management and evolutionary phylogenetics studies, and employs a plugin-based system that integrates a number of useful phylogenetic and bioinformatic tools.

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An advanced version of the Molecular Evolutionary Genetics Analysis software, which currently contains facilities for building sequence alignments, inferring phylogenetic histories, and conducting molecular evolutionary analysis, is released, which enables the inference of timetrees, as it implements the RelTime method for estimating divergence times for all branching points in a phylogeny.

MEGA-CC provides users with access to all the computational analyses available through MEGA's graphical user interface version, including methods for multiple sequence alignment, substitution model selection, evolutionary distance estimation, phylogeny inference, substitution rate and pattern estimation, tests of natural selection and ancestral sequence inference.

In this program, various methods for estimating evolutionary distances from nucleotide and amino acid sequence data, three different methods of phylogenetic inference (UPGMA, neighbor-joining and maximum parsimony) and two statistical tests of topological differences are included.

This work gives an algorithm to infer speciation and duplication events on a gene tree by comparison to a trusted species tree, and shows empirically, using 1750 gene trees constructed from the Pfam protein family database, that it appears to be a practical (and often superior) algorithm for analyzing real gene trees.

It is concluded that it is best to use larger alignments, because adding both genes and species to the alignment augments the number of genes available for estimating divergence events deep in the tree and improves their time estimates.

The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.

RelTime is presented, a method that estimates relative times of divergences for all branching points (nodes) in very large phylogenetic trees without assuming a specific model for lineage rate variation or specifying any clock calibrations.

The improvements the SILVA taxonomy has undergone in the last 3 years are described, focusing on the curation process, the various resources used for curation and the comparison of the SILva taxonomy with Greengenes and RDP-II taxonomies.

A global timetree of life synthesized from 2,274 studies representing 50,632 species and examined the pattern and rate of diversification as well as the timing of speciation suggests that speciation and diversification are processes dominated by random events and that adaptive change is largely a separate process.

MUSCLE offers a range of options that provide improved speed and / or alignment accuracy compared with currently available programs, and a new option, MUSCLE-fast, designed for high-throughput applications.

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