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Data
   Input Data Format Dialog
   Missing data or invalid distances in the matrix
   Setup/Select Genes & Domains Dialog
    Missing
       Input Data Format Dialog
       Missing data or invalid distances in the matrix
Data | Data Explorer
   Close Data
   Data Explorer
   Export Data
Data | Quit Data Viewer
Data | Select Genetic Code Table
   Select Genetic Code Table
   Select Genetic Code Table (in Sequence Data Explorer)
Data | Select Preferences
   Handling Gaps and Missing Data
   Include Codon Positions
   Include Labeled Sites
   Select Preferences
Data | Setup/Select Genes
   Setup/Select Genes & Domains
   Setup/Select Genes & Domains (in Sequence Data Explorer)
Data | Setup/Select Taxa
   Setup/Select Taxa & Groups
   Setup/Select Taxa & Groups (in Sequence Data Explorer)
Data | Translate/Untranslate
Data | Write Data
Data Description Window
Data Explorer
   Computing statistics on only highlighted sites in Data Explorer
   Data Explorer
   Data Menu (in sequence Data Explorer)
   Export Data
   No Common Sites
   Setup/Select Taxa & Groups Dialog
Data File Parsing Error
Data menu
   Data Menu
   Data Menu (in sequence Data Explorer)
   Export Data
   Guide to Notations Used
   Select Genetic Code Table
   Select Genetic Code Table (in Sequence Data Explorer)
   Setup/Select Genes & Domains (in Sequence Data Explorer)
   Setup/Select Taxa & Groups (in Sequence Data Explorer)
Data Menu in Alignment Explorer
Data Type
   Data Explorer
   Input Data Format Dialog
Datafile
DataFormat
Dataset
   Close Data
   Codon Usage
   Inapplicable Computation Requested
   Keywords for Format Statement (Distance data)
   Not Enough Groups Selected
   Not Enough Taxa Selected
   Nucleotide and Amino Acid Compositions
   Sequence Data Explorer
   Translate/Untranslate (in Sequence Data Explorer)
DataType
   Keywords for Format Statement (Distance data)
   Keywords for Format Statement (Sequence data)
   Rules for Format Statement
Dayhoff 1979
Dayhoff and JTT distances Gamma rates
Dayhoff distance
   Dayhoff 1978
   Eck and Dayhoff 1966
   Gamma distance (Amino acids)
Dayhoff Distance Could Not Be Computed
Dayhoff Model
Define/Edit/Select
Defining Genes
Defining Groups
DefiningTaxa
Description Statement Rules
Disclaimer
Discrete-character
Disparity Index
Display
    UPGMA
Display | Color
Display | Restore Input Order
Display | Show
Display | Show Group Names
Display | Show Sequence Names
Display | Sort Sequences
   Sort Sequences
   Sort Sequences As per Taxa/Group Organizer
   Sort Sequences by Group and Sequence Names
   Sort Sequences by Group Name
   Sort Sequences By Sequence Name
Display | Use Identical Symbol
Display font
Display Menu
   Display Menu (in Distance Data Explorer)
   Display Menu (in Distance Matrix Explorer)
   Display Menu (in Sequence Data Explorer)
Display Menu in Alignment Explorer
Display Newick Trees from File
Display Saved Tree Session
Distance Computation
Distance Correction Failed
Distance Data Explorer
   Average Menu (in Distance Data Explorer)
   Display Menu (in Distance Data Explorer)
   Distance Data Explorer
   Distance Data Subset Selection
   Distance Matrix Explorer
   File Menu (in Distance Data Explorer)
   File Menu (in Distance Matrix Explorer)
Distance Data Formats
Distance Data Subset Selection
Distance Display Precision
   Distance Data Explorer
   Distance Matrix Explorer
Distance estimates
Distance Matrix Dialog
   Gamma Distance Failed Because p > 0.99
   Jukes-Cantor Distance Failed
   Kimura Distance Failed
   p distance is found to be > 1
   Poisson Correction Failed because p > 0.99
   Tajima-Nei Distance Could Not Be Computed
   Tamura (1992) Distance Could Not Be Computed
   Tamura-Nei Distance Could Not Be Computed
Distance Matrix Explorer
   Average Menu (in Distance Data Explorer)
   Average Menu (in Distance Matrix Explorer)
   Display Menu (in Distance Matrix Explorer)
   Distance Matrix Explorer
   File Menu (in Distance Matrix Explorer)
Distance menu
   Compute Sequence Diversity
   Distances Menu
   Finding number of sites in pairwise comparisons
   Main MEGA Window
Distance Model Options
Distance Options
   Analysis Preferences (Fisher's Exact Test)
   Analysis Preferences (Z-test of Selection)
Distances
   Get more information about the codon based Z-test for selection
   Models for estimating distances
   Sequence Data Explorer
   Translate/Untranslate (in Sequence Data Explorer)
Distances | Choose Model
Distances | Compute Between Groups Means.Choose
Distances | Compute Net Between Groups Means.Choose
Distances | Compute Overall Mean
Distances | Compute Pairwise
Distances | Compute Sequence Diversity
Distances | Compute Within Groups Means.Choose
Distances Display Box
Distances Menu
Divergence Time
   Scale Bar tab (in Options dialog box)
   Subtree Menu (in Tree Explorer)
Divergence Time Dialog Box
DNA
   Alignment Gaps and Sites with Missing Information
   Color Cells
   Data Explorer
   Display Menu (in Sequence Data Explorer)
   Importing Data From Other Formats
   Keywords for Format Statement (Sequence data)
   MEGA Format
   Nucleotide and Amino Acid Compositions
   Phylogenetic Inference
   Sequence Data Explorer
    coding
    reading data from other formats
DNA/RNA
   Invalid special symbol in molecular sequences
   IUPAC single letter codes
Do BLAST Search
Domain Editor
Domains
   Amino Acid Composition
   Codon Usage
   Nucleotide Composition
   Nucleotide Pair Frequencies
   Setup/Select Genes & Domains
   Setup/Select Genes & Domains (in Sequence Data Explorer)
   Writing Command Statements for Defining Genes and Domains
Domains Cannot Overlap
Domains Dialog
Drag-and-drop
Drosophila mitochondrial genetic code table

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