Index words list

OLS branch length estimates
Only 4-fold degenerate sites
Only 4-fold degenerate sites:Writing
Only highlighted sites
Only Nei-Gojobori
Open
Open A File
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)
   Tree tab (in Options dialog box)
Options dialog:MP Tree Tab
Options dialog:quit
Order
   Setup/Select Taxa & Groups Dialog
   View Menu (in Tree Explorer)
Order:taxa
   Setup/Select Taxa & Groups Dialog
   View Menu (in Tree Explorer)
OTUs
   Phylogenetic Inference
   Rules for Taxa Names
   UPGMA
Outgroup
Outgroup taxa
Output file
Overview

P-distance
   p distance is found to be > 1
   p-distance (Amino acids)
   p-distance (Nucleotide)
Page and Holmes 1998
Pairwise comparisons
Pairwise Deletion
Pairwise Distance Data
Pairwise menu
Pairwise-Deletion
Pamilo-Bianchi-Li
   Kumar Method
   Pamilo-Bianchi-Li Method
Pamilo-Bianchi-Li Method
Parsimony-informative
Partial-Deletion Option
Paste
Pattern Menu
Pauline and Henikoff 2010
PAUP 3.0
PAUP 4.0
Phenylalanine
Phy
PHYLIP
PHYLIP 3.0
Phylogenetic
   Alignment Gaps and Sites with Missing Information
   Analysis Preferences (Maximum Parsimony)
   Analysis Preferences (Minimum Evolution)
   Analysis Preferences (NJ/UPGMA)
   Bootstrap Test of Phylogeny
   Citing MEGA in Publications
   Condensed Trees
   Fitch and Margoliash 1967
   Hillis and Bull 1993
   Maximum Parsimony (Construct Phylogeny)
   MEGA Format
   Minimum Evolution (Construct Phylogeny)
   Models for estimating distances
   Monophyletic
   Phylogenetic Inference
   Phylogeny Menu
   Rzhetsky and Nei 1993
   Sourdis and Krimbas 1987
   Sourdis and Nei 1988
   Tateno et al. 1982
Phylogenetic Inference
Phylogenetic:construct
   Minimum Evolution (Construct Phylogeny)
   Phylogenetic Inference
Phylogenies
   Phylogenetic Inference
   Sequence Data Explorer
   Translate/Untranslate (in Sequence Data Explorer)
Phylogeny | Any
Phylogeny | Bootstrap Test
Phylogeny | Display Saved Tree Session.Use
Phylogeny | Maximum Parsimony
Phylogeny | Minimum Evolution
Phylogeny | Neighbor-Joining
Phylogeny | UPGMA.This
Phylogeny menu
   Main MEGA Window
   Phylogeny Menu
Poisson
   Gamma distance (Amino acids)
   Poisson Correction (PC) distance
   Poisson Correction Failed because p > 0.99
Poisson Correction distance
Poisson Correction Failed
Polypeptide
Position
   Code Table Editor
   Sequence Data Subset Selection
Position:codon
Prediction Data Tab
Preface
Print
   Exit
   Print (in Text Editor)
Print dialog
Printer Setup
   File Menu (in Tree Explorer)
   Printer Setup
Program
Program:uncompress
Proline
Protein parsimony
Pseudorandom number generator
Purdom et al. 2000
Pyrimindine

Query Databanks
Quit Data Viewer
   Data Menu (in sequence Data Explorer)
   Quit Data Viewer
Quit Options dialog
Quit Viewer
   File Menu (in Distance Data Explorer)
   File Menu (in Distance Matrix Explorer)

RAM
Rate
Read
Read:DNA
Relative Rate
RelTime Tool
Removing
Removing:taxon
Reopen Data
Replace
Reporting Bugs
Resampled dataset
Resampling
   Bootstrap Test of Phylogeny
   Codon Based Z-Test (large sample)
   Large Sample Tests of Selection
Residue-by-residue
Restore Input Order
RNA
   Data Explorer
   Keywords for Format Statement (Sequence data)
RSCU
Rules
   Rules for Description Statement
   Rules for Format Statement
   Rules for Taxa Names
   Rules for Title Statement
Rules:Description Statement
Rules:Format Statement
Rules:Taxa Names
Rules:Title Statement