0-fold site

2-Dimensional Data Grid
   Distance Data Explorer
   Distance Matrix Explorer
   Sequence Data Explorer
2-fold site
2S-fold site
2V-fold site

4-fold site
   Kumar Method
   Li-Wu-Luo Method
   Pamilo-Bianchi-Li Method
   Writing only 4-fold degenerate sites to an output file

ABI File Format
About BLAST
About CLUSTALW
About dialog
   About
   Help Menu
About MUSCLE
Acknowledgements
Add button
Add taxa
   Setup/Select Genes & Domains Dialog
   Setup/Select Taxa & Groups Dialog
Add/Insert
Add/Remove Programs
Adding/Modifying Genetic Code Tables
Adzubhei et al. 2010
Alanine
Aligning coding sequences via protein sequences
Alignment Builder
Alignment Gap
   Alignment Gaps and Sites with Missing Information
   Alignment Gaps and Sites with Missing Information
   Input Data Format Dialog
Alignment Menu
Alignment Menu in Alignment Explorer
Alignment session
Amino Acid Compositions
   Amino Acid Composition
   Nucleotide and Amino Acid Compositions
Analysis Options
Analysis Preferences
   Analysis Preferences (Distance Computation)
   Analysis Preferences (Fisher's Exact Test)
   Analysis Preferences (Maximum Parsimony)
   Analysis Preferences (Minimum Evolution)
   Analysis Preferences (NJ/UPGMA)
   Analysis Preferences (Z-test of Selection)
Analysis Preferences dialog
Analysis Preferences Estimate Selection for each Codon
Analysis Preferences Maximum Likelihood
Analysis Preferences/Options dialog
Analyze User Tree by Least Squares
Analyze User Tree by Maximum Likelihood
Analyze User Tree by Parsimony
Arrange Taxa
ASCII
   Font (in Text Editor)
   General Considerations (Sequence Data)
   MEGA Format
   Save As (in Text Editor)
   Text File Editor and Format Converter
ASCII-text
ASCII:editing
Asparagine
Aspartic Acid
Assigning
Assigning:exons
Average Menu
   Average Menu (in Distance Data Explorer)
   Average Menu (in Distance Matrix Explorer)

Basic Sequence Statistics
BCL
Between Groups
Bidirectionally
Bifurcating Tree
Blank Names Are Not Permitted
BLAST Search
Bootstrap method
Bootstrap method:compute standard error
Bootstrap Test
Bootstrap Test of Phylogeny
Branch Length
Branch Line
Branch Swap Filter
Branch tab
Branch-and-bound
   Analysis Preferences (Maximum Parsimony)
   Maximum Parsimony (MP) Method
Browse Databanks
Bugs
Bugs:Reporting
Built-in Genetic Codes

Calibration Dialog
Calibration File Format
Caption Expert
Captions
Categorize
Categorize:taxa
Change Font
   Display Menu (in Distance Data Explorer)
   Display Menu (in Distance Matrix Explorer)
Change Font dialog box
Change Font.Display
Circle
Citing MEGA in Publications
Classroom
Clipboard
   Copy (in Text Editor)
   Cut (in Text Editor)
Close Data
Close-Neighbor-Interchange
CLUSTAL
ClustalW
CLUSTALW Options DNA
CLUSTALW Options Protein
CNI
   Close-Neighbor-Interchange (CNI)
   Maximum Parsimony (Construct Phylogeny)
Code Table
Code Table Editor
Coding
   Keywords for Command Statements (Genes/Domains)
   Keywords for Format Statement (Sequence data)
   Sequence Data Explorer
   Setup/Select Genes & Domains Dialog
Coding:DNA
Codon
   Analysis Preferences (Distance Computation)
   Analysis Preferences (Fisher's Exact Test)
   Analysis Preferences (Maximum Parsimony)
   Analysis Preferences (Minimum Evolution)
   Analysis Preferences (NJ/UPGMA)
   Analysis Preferences (Z-test of Selection)
   Basic Sequence Statistics
   Built-in Genetic Codes
   Code Table Editor
   Codon Usage
   Codon Usage
   Computing Statistical Attributes (Genetic Code)
   Export Data (in Sequence Data Explorer)
   Li-Wu-Luo Method
   Menus in MEGA are so short, where are all the options?
   Nucleotide and Amino Acid Compositions
   Select Genetic Code Table Dialog
   Sequence Data Explorer
   Setup/Select Genes & Domains Dialog
   Writing only 4-fold degenerate sites to an output file
Codon based Z-test
Codon Usage
   Codon Usage
   Codon Usage
Codon:find
Codon:inclusion/exclusion
   Analysis Preferences (Distance Computation)
   Analysis Preferences (Fisher's Exact Test)
   Analysis Preferences (Maximum Parsimony)
   Analysis Preferences (Minimum Evolution)
   Analysis Preferences (NJ/UPGMA)
   Analysis Preferences (Z-test of Selection)
Codon:position
Color Cells
Column Sizer
   Distance Data Explorer
   Distance Matrix Explorer
Command Statements
   Keywords for Command Statements (Genes/Domains)
   Writing Command Statements for Defining Genes and Domains
   Writing Command Statements for Defining Groups of Taxa
Command Statements:Keywords
Command Statements:Writing
   Writing Command Statements for Defining Genes and Domains
   Writing Command Statements for Defining Groups of Taxa
Common Features
Common Sites
Complete-Deletion
Complex 2-fold sites
Composition Distance
Compute Between Groups Means
Compute MCL Substitution Matrix
Compute MCL Transversion/Transition bias
Compute Menu
Compute Net Between Groups Means
Compute Overall Mean
Compute Pairwise
Compute Sequence Diversity
Compute standard error
Compute standard error:Bootstrap method
Compute Within Groups Mean
Computing
   Computing Statistical Attributes (Genetic Code)
   Computing statistics on only highlighted sites in Data Explorer
   Gamma distance (Amino acids)
   Kumar Method
Computing Statistical Quantities for Nucleotide Sequences
Computing the Gamma Parameter (a)
Computing:Statistical Attributes
Computing:statistics
Condensed Trees
Construct
   Maximum Parsimony (MP) Method
   Minimum Evolution (Construct Phylogeny)
   Neighbor Joining (Construct Phylogeny)
   Phylogenetic Inference
   UPGMA (Construct Phylogeny)
Constructing a Time Tree ML
Constructing Likelihood Trees
Constructing Trees and Selecting OTUs from Nucleotide Sequences
Constructing Trees from Distance Data
Convert To MEGA Format Main File Menu
Copy
Copyright
CPU
Create New Folder
Creating Data Captions with Caption Expert
Creating Multiple Sequence Alignments
CSV
   Distance Data Explorer
   Distance Matrix Explorer
   Options dialog box
   Statistics Menu (in Sequence Data Explorer)
Curved
Cut
Cutoff Values Tab
Cysteine

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