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MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses.
- tutorial
Install Mega then Convert Phylip File to Mega Format and...
- features
MEGA is an integrated tool for conducting automatic and...
- documentation
Help docs and user manuals for the MEGA genetics analysis...
- feedback
Thank you for taking the time to submit a suggestion. User...
- walk through
This walk-through provides several brief tutorials that...
- books / articles
MEGA Software Celebrates Silver Anniversary Caspermeyer J...
- Older Versions
By downloading MEGA, you are agreeing not to redistribute...
- Downloads
For users with macOS systems using M1 chips, the Windows or...
- tutorial
For users with macOS systems using M1 chips, the Windows or Linux version of MEGA can be run using virtualization or emulation software. Several options for doing so are available including Parallels, Crossover, and VMWareFusion.
MEGA is an integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. MEGA 4 has been tested on the following Microsoft Windows® operating systems:
- Outline
- MEGA
- Phylogenetics
- Why Create Phylogenetic Trees?
- Parts of a Tree
- Steps to Create Phylogenetic Trees
- Character‐based
- Distance‐based
- Character‐based: Parsimony
- Character‐based: Probabilistic
- Some Tips
- Phylogenetic Tree Software
- A More Comprehensive Listing of Phylogeny Programs:
MEGA Features Background on Phylogenetic Trees Brief Overview of Tree Building Methods MEGA Demo
Easy‐to‐use software with multiple features Features: Aligning sequences Estimating evolutionary distances Building trees using several methods Testing tree reliability Marking Genes/Domains Testing for selection Computing sequence statistics
Study of evolutionary relationship Phylogenetic tree is a graphical representation of the evolutionary relationships Phylogeny of... Species Strains Genes Metabolic Pathways Trees can be inferred by morphology or molecular information
Reconstruct evolutionary history Draw conclusions of biological functions which might not be apparent Pre‐computed trees (eg. Ensembl, Pfam) might not include genes or species of interest
Nodes: taxonomic units (eg. genes, species, Internal: ancestral state etc.) Bifurcating Multifurcating External: Operational Taxonomic Units (OTUs) Branches: relationships among the taxonomic units (ie. ancestor‐descendent relationship). Clade Branch Length: number of changes that have occurred Topology: branching patt...
Identify and acquire the sequences that are to be included on the tree Align the sequences (MSA using ClustalW, T‐Coffee, MUSCLE, etc.) Estimate the tree by one of several methods Draw the tree and present it From Hall, B.G. (p.3 ‐ see Further Reading Slide)
‐Parsimony ‐Probabilistic Character State Matrix Species A ACTTC Species B AGTTC Species C CGTAC Species D CCTAC
Unweighted Pair Group Method with Arithmetic mean (UPGMA) Neighbor‐Joining (NJ) Start with all taxa in a single node and decompose with each iteration Pair of nodes pulled out (grouped) at each iteration are chosen so that the total length of the branches on the tree is minimized Mutation rates are not con...
Preferred phylogenetic tree is the one with the fewest evolutionary steps Identify informative sites For each possible tree, calculate the number of changes at each informative site Sum total number of changes for each possible tree, the tree with the smallest number of changes is selected as the most li...
Maximum Likelihood At each site, the likelihood is determined by evaluating the probability that a certain evolutionary model (eg. BLOSSUM or PAM matrices) has generated the observed data. The likelihood’s for each site are then multiplied to provide likelihood for each tree Choose the tree with maximum ...
Use more than one method Use more than one software package Examine more than one tree if multiple trees are generated Bootstrap your data Homology vs Homoplasy Consider another intermediate taxa to resolve relationship, if needed
PHYLIP (the PHYLogeny Inference Package): http://evolution.genetics.washington.edu/phylip.html PAUP*: http://paup.csit.fsu.edu MrBayes: http://mrbayes.csit.fsu.edu MEGA(Molecular Evolutionary Genetic Analysis) http://www.megasoftware.net
http://evolution.genetics.washington.edu/phylip/software.html *Commercial software
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Building Trees From Sequence Data. In this tutorial, we will illustrate the procedures for building trees and in-memory sequence data editing, using the commands available in the Data and Phylogeny menus. We will be using the "Crab_rRNA.meg" file which can be found in the MEGA/Examples directory.
Apr 23, 2021 · MEGA’s Tree Explorer (A) is a feature-rich, versatile viewer of phylogenies that provides many interactive exploration and customization facilities. In MEGA11, the new side toolbar of Tree Explorer makes formatting, rearrangement, and tree exploration tools more accessible and intuitive.
Install Mega then Convert Phylip File to Mega Format and Construct NJ Tree. Introduction to MEGA. Testing Different Tree Methods and Models. Align Sequences then Construct a Fossil Calibrated Maximum Likelihood Tree. Align Sequences then Construct Maximum Likelihood Tree.
![A phylogenetic tree constructed in MEGA X software [16] using the ...](https://in.images.search.yahoo.com/search/images?p=mega+software+for+phylogenetic+tree&ei=UTF-8&xargs=0&fr=fp-hotsearch-hifi-in&th=98.5&tw=97.3&imgurl=https%3A%2F%2Fwww.researchgate.net%2Fpublication%2F338461344%2Ffigure%2Ffig3%2FAS%3A962203649839134%401606418635681%2FA-phylogenetic-tree-constructed-in-MEGA-X-software-16-using-the-neighbor-joining-method.png&rurl=https%3A%2F%2Fwww.researchgate.net%2Ffigure%2FA-phylogenetic-tree-constructed-in-MEGA-X-software-16-using-the-neighbor-joining-method_fig3_338461344&size=103KB&name=A+phylogenetic+tree+constructed+in+MEGA+X+software+%5B16%5D+using+the+...&oid=3&h=862&w=850&turl=https%3A%2F%2Ftse1.mm.bing.net%2Fth%3Fid%3DOIP.GpvlEhzxc90XhFXjri7LawHaHg%26pid%3DApi%26rs%3D1%26c%3D1%26qlt%3D95%26w%3D97%26h%3D98&tt=A+phylogenetic+tree+constructed+in+MEGA+X+software+%5B16%5D+using+the+...&sigr=vfY9bnEM3TiI&sigit=u1QeHdrdC8MI&sigi=5VTt.3fHpnQf&sign=dOYn29sGFB5I&sigt=dOYn29sGFB5I "A phylogenetic tree constructed in MEGA X software [16] using the ...")
