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
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
Alanine
Aligning coding sequences via protein sequences
Alignment Builder
Alignment Explorer/CLUSTAL
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 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/Options dialog
Arrange Taxa
ASCII
   Font (in Text Editor)
   General Considerations (Sequence Data)
   MEGA Format
   Save As (in Text Editor)
   Text File Editor and Format Converter
    editing
ASCII-text
Asparagine
Aspartic Acid
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
    compute standard error
Bootstrap Test
Bootstrap Test of Phylogeny
Branch-and-bound
   Analysis Preferences (Maximum Parsimony)
   Maximum Parsimony (MP) Method
Branch Length
Branch Line
Branch tab
Browse Databanks
Bugs
    Reporting
Built-in Genetic Codes

Caption Expert
Captions
Categorize
    taxa
Change Font
   Display Menu (in Distance Data Explorer)
   Display Menu (in Distance Matrix Explorer)
Change Font dialog box
Change Font.Display
Choose Model
Circle
Citing MEGA in Publications
Classroom
Clipboard
   Copy (in Text Editor)
   Cut (in Text Editor)
Close-Neighbor-Interchange
Close Data
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
    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
   Select Preferences
   Sequence Data Explorer
   Setup/Select Genes & Domains Dialog
   Writing only 4-fold degenerate sites to an output file
    find
    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)
    position
Codon based Z-test
Codon Usage
   Codon Usage
   Codon Usage
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
    Keywords
    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 Menu
Compute Net Between Groups Means
Compute Overall Mean
Compute Pairwise
Compute Sequence Diversity
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
    Statistical Attributes
    statistics
Computing Statistical Quantities for Nucleotide Sequences
Computing the Gamma Parameter (a)
Condensed Trees
Construct
   Maximum Parsimony (MP) Method
   Minimum Evolution (Construct Phylogeny)
   Neighbor Joining (Construct Phylogeny)
   Phylogenetic Inference
   UPGMA (Construct Phylogeny)
Construct Phylogeny
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
Curved
Cut
Cutoff Values Tab
Cysteine

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