<<

Name
   Code Table Editor
   Display Menu (in Distance Matrix Explorer)
   Distance Data Explorer
   Distance Matrix Explorer
   Open Data
    sequences/groups
       Distance Data Explorer
       Distance Matrix Explorer
    taxa
NCBI
Nei-Gojobori
   Computing Statistical Attributes (Genetic Code)
   Modified Nei-Gojobori Method
Nei-Gojobori Method
Nei et al. 1998
Neighbor-Joining
Neighbor Joining
Neighbor Joining Construct Phylogeny
Net Between Groups
   Average Menu (in Distance Data Explorer)
   Average Menu (in Distance Matrix Explorer)
Neutrality
    Tajima's Test
    Tests | Tajima's Test
New
Newick Format
Nex
Nexus/PAUP
NJ
   Condensed Trees
   Minimum Evolution
   Minimum Evolution (Construct Phylogeny)
   Neighbor Joining (Construct Phylogeny)
   Neighbor-Joining (NJ) Method
NJ/UPGMA
Noncoding
   Export Data (in Sequence Data Explorer)
   Keywords for Command Statements (Genes/Domains)
   Keywords for Format Statement (Sequence data)
   Writing Command Statements for Defining Genes and Domains
   Writing Command Statements for Defining Groups of Taxa
Nonsynonymous
   Analysis Preferences (Fisher's Exact Test)
   Analysis Preferences (Z-test of Selection)
   Codon Based Z-Test (large sample)
   Computing Statistical Attributes (Genetic Code)
   Fisher's Exact Test Has Failed
   Jukes-Cantor Distance Failed
   Kumar Method
   Large Sample Tests of Selection
   Li-Wu-Luo Method
   Modified Nei-Gojobori Method
   Nei-Gojobori Method
   Pamilo-Bianchi-Li Method
Nonsynonymous site
   Codon Based Fisher's Exact Test
   Codon Based Z-Test (large sample)
   Kumar Method
   Large Sample Tests of Selection
   Li-Wu-Luo Method
   Pamilo-Bianchi-Li Method
Notations Used
Notepad
NSeqs
   Keywords for Format Statement (Distance data)
   Keywords for Format Statement (Sequence data)
NSites
NT
NTaxa
   Keywords for Format Statement (Distance data)
   Keywords for Format Statement (Sequence data)
Nucleotide
Nucleotide-by-nucleotide
Nucleotide-by-nucleotide site
Nucleotide Composition
Nucleotide Pair Frequencies
   Nucleotide Pair Frequencies
   Nucleotide Pair Frequencies
Number
   Analysis Preferences (Fisher's Exact Test)
   Codon Based Z-Test (large sample)
   Computing Statistical Attributes (Genetic Code)
   Distance Matrix Explorer
   Finding number of sites in pairwise comparisons
   Fisher's Exact Test Has Failed
   Kimura 2-parameter distance
   Kimura gamma distance
   Kumar Method
   Large Sample Tests of Selection
   Li-Wu-Luo Method
   Minimum Evolution
   Modified Nei-Gojobori Method
   Nei-Gojobori Method
   Neighbor Joining (Construct Phylogeny)
   Neighbor-Joining (NJ) Method
   Pamilo-Bianchi-Li Method
   Tamura 3-parameter distance
   Tamura-Nei distance
   Tamura-Nei gamma distance
    0-fold
       Kumar Method
       Li-Wu-Luo Method
       Pamilo-Bianchi-Li Method
    4-fold
       Kumar Method
       Li-Wu-Luo Method
       Pamilo-Bianchi-Li Method
    codons
    Finding
    nonsynonymous
       Codon Based Z-Test (large sample)
       Computing Statistical Attributes (Genetic Code)
       Fisher's Exact Test Has Failed
       Kumar Method
       Large Sample Tests of Selection
       Li-Wu-Luo Method
       Modified Nei-Gojobori Method
       Nei-Gojobori Method
       Pamilo-Bianchi-Li Method
    Sites
       Modified Nei-Gojobori Method
       Nei-Gojobori Method
    taxa
       Distance Matrix Explorer
       Minimum Evolution
       Neighbor Joining (Construct Phylogeny)
       Neighbor-Joining (NJ) Method
    transversional
       Kimura 2-parameter distance
       Kimura gamma distance
       Tamura 3-parameter distance
       Tamura-Nei distance
       Tamura-Nei gamma distance

OLS branch length estimates
Only 4-fold degenerate sites
    Writing
Only highlighted sites
Only Nei-Gojobori
Open
Open Data
Open Saved Alignment Session
Operational Taxonomic Units
Options dialog
   Branch tab (in Options dialog box)
   Labels tab (in Options dialog box)
   Maximum Parsimony (Construct Phylogeny)
   Options dialog box
   Options dialog box (in Tree Explorer)
   Scale Bar tab (in Options dialog box)
   Select Preferences
   Tree tab (in Options dialog box)
    MP Tree Tab
    quit
Order
   Setup/Select Taxa & Groups Dialog
   View Menu (in Tree Explorer)
    taxa
       Setup/Select Taxa & Groups Dialog
       View Menu (in Tree Explorer)
OTUs
   Phylogenetic Inference
   Rules for Taxa Names
   UPGMA
Outgroup
Outgroup taxa
Output file

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