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MEGA Tutorial

This document provides instructions for a phylogeny assignment using the program MEGA. It outlines downloading required materials, running analyses to build a phylogenetic tree from sequence data, answering questions, and attaching the tree to the assignment. A quick tutorial walks through opening MEGA, loading sequence data, constructing a maximum parsimony tree with bootstrapping, computing the analysis, rooting and printing the tree, and answering analysis questions. Help sessions are available from a teaching assistant. The assignment is due at the start of Lab 3 and late assignments will not be accepted.

Uploaded by

Dennedy Yrvin Corcega
Copyright
© © All Rights Reserved
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
261 views

MEGA Tutorial

This document provides instructions for a phylogeny assignment using the program MEGA. It outlines downloading required materials, running analyses to build a phylogenetic tree from sequence data, answering questions, and attaching the tree to the assignment. A quick tutorial walks through opening MEGA, loading sequence data, constructing a maximum parsimony tree with bootstrapping, computing the analysis, rooting and printing the tree, and answering analysis questions. Help sessions are available from a teaching assistant. The assignment is due at the start of Lab 3 and late assignments will not be accepted.

Uploaded by

Dennedy Yrvin Corcega
Copyright
© © All Rights Reserved
Available Formats
Download as PPTX, PDF, TXT or read online on Scribd
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Phylogeny Assignment - Materials

Download required reading Understanding


evolutionary trees (via Google search OR
library search)
Acquire access to the computer program
MEGA (download program OR UTSC
computer labs)
Have access to MEGA online manual (MEGA
homepage)
Download Vertebrate_CytB_Fall_2017.meg
via Blackboard
Phylogeny Assignment - Overview
Name and student number on both answer pages
AND your phylogenetic tree
Read the assignment carefully

PART 1
Instructions will walk you through the necessary
steps to run your data analysis and build your
phylogenetic tree
Answer all questions
Attach a copy of your phylogenetic tree to your
answer page (see question 3)
A quick tutorial
MEGA A quick tutorial

PART 1A
Open the MEGA program
Select File, Open a
File/Session
Find file that you downloaded
Select that file and click Open
Open file marked TA
Answer questions 1-2
MEGA A quick tutorial
PART 1B
Go to the Data tab and press
'quit data viewer'
Press 'Phylogeny', then
'Construct maximum
parsimony tree.'
Choose the Bootstrap
method for the test type and
set the No. of Bootstrap
Replications to 1000.
Choose Use all sites for
Gaps/Missing Data
Treatment
Choose Max-mini Branch-&-
bound for the MP search
method.
Press 'Compute'.
MEGA A quick tutorial
NOTE: The data file that you will run for your
analysis will take ~45 minutes to run
TIP: Read the assigned article while your
analysis is running or work on Part 2

Did you know Phylogenetic


analyses can run for hours,
days, weeks, or months
MEGA A quick tutorial
PART 1B Continued
Once the run is complete, select the OG
branch and root the tree using the second
icon from the top Place root on branch
Print the original tree, making sure to add
bootstrap values by clicking on the second last
icon on the left side bar (Display of node
statistics).
Answer questions 3-9
MEGA A quick tutorial
PART 2
Construct phylogenetic tree from character
matrix
Answer all questions

Once you have completed your assignment


be sure to check that you have answered all
the questions and attached your tree.
Phylogeny Assignment Help
Nikki Alber (BIOhelp TA for labs/assignments)
will provide help sessions
An announcement will be posted on the course
Blackboard page with all details (time, location, +
information on how to sign up)
Phylogeny Assignment Forum on Discussion Board
REMINDER
Your Phylogeny assignment is due at the
beginning of your Lab 3.
It will be collected as you enter the lab, be
sure to have it ready.
No late assignments will be accepted !

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