#priority	category	defined	glossary_index	concept
1	basic	(defined)	4.10	Branch Support
1	basic	(defined)	4.100	Trait
1	basic	(defined)	4.103	Tree
1	basic	(defined)	4.104	Unresolved
1	basic	(defined)	4.11	Character
1	basic	(defined)	4.12	Character-State
1	basic	(defined)	4.13	Character-State Data Matrix
1	basic	(defined)	4.15	Cladogram
1	basic	(defined)	4.21	Derived
1	basic	(defined)	4.22	Descendant
1	basic	(defined)	4.23	Dichotomy
1	basic	(defined)	4.27	Edge
1	basic	(defined)	4.3	Ancestor
1	basic	(defined)	4.30	Fully Resolved
1	basic	(defined)	4.31	Gap
1	basic	(defined)	4.35	Homology
1	basic	(defined)	4.39	HTU
1	basic	(defined)	4.4	Apomorphy
1	basic	(defined)	4.40	Hypothetical Taxonomic Unit
1	basic	(defined)	4.41	Indel
1	basic	(defined)	4.44	Leaf node
1	basic	(defined)	4.48	Monophyly
1	basic	(defined)	4.49	Most Recent Common Ancestor
1	basic	(defined)	4.50	MRCA
1	basic	(defined)	4.55	Network
1	basic	(defined)	4.59	Operational Taxonomic Unit
1	basic	(defined)	4.6	Bifurcation
1	basic	(defined)	4.62	OTU
1	basic	(defined)	4.63	Outgroup
1	basic	(defined)	4.68	Phylogenetic Tree
1	basic	(defined)	4.69	Phylogenetic Tree Topology
1	basic	(defined)	4.7	Bipartition
1	basic	(defined)	4.73	Polymorphism
1	basic	(defined)	4.75	Primitive
1	basic	(defined)	4.8	Bootstrap Support
1	basic	(defined)	4.83	Root
1	basic	(defined)	4.87	State
1	basic	(defined)	4.9	Branch
1	basic	(defined)	4.90	Subtree
1	basic	(defined)	4.95	Taxon
1	basic	(defined)	4.96	Taxonomic Rank
1	basic	(defined)	4.98	Terminal Node
1	basic	(defined)	4.99	Topology
1	basic	(undefined)	4.2	Basal
1	basic	(undefined)	4.25	lineage
1	basic	(undefined)	4.27	Missing Data
1	basic	(undefined)	4.29	Polytomy
1	basic	(undefined)	4.42	Unrooted
2	external	(defined)	4.60	Organismal Taxonomy
2	external	(defined)	4.77	Rank
2	external	(defined)	4.86	Species Tree
2	external	(defined)	4.97	Taxonomy
2	external	(undefined)	4.16	Family alignment
2	external	(undefined)	4.37	Sequence Family
2	external	(undefined)	4.38	Species
2	transformations	(defined)	4.101	Transition, disambiguation
2	transformations	(defined)	4.102	Transition Model
2	transformations	(defined)	4.14	Clade
2	transformations	(defined)	4.17	Convergence
2	transformations	(defined)	4.18	Convergent Evolution
2	transformations	(defined)	4.2	Analogy
2	transformations	(defined)	4.20	Deletion
2	transformations	(defined)	4.28	Evolutionary Transition
2	transformations	(defined)	4.34	HGT
2	transformations	(defined)	4.38	Horizontal Gene Transfer (HGT)
2	transformations	(defined)	4.42	Insertion
2	transformations	(defined)	4.43	Lateral Gene Transfer
2	transformations	(defined)	4.45	LGT
2	transformations	(defined)	4.5	Atavism
2	transformations	(defined)	4.57	Nucleotide Transition
2	transformations	(defined)	4.58	Nucleotide Transversion
2	transformations	(defined)	4.70	Phylogeny
2	transformations	(defined)	4.79	Reconstruction
2	transformations	(defined)	4.80	Replacement
2	transformations	(defined)	4.81	Reversion
2	transformations	(defined)	4.82	Reversal
2	transformations	(defined)	4.88	Step Matrix
2	transformations	(defined)	4.89	Substitution
2	transformations	(undefined)	4.10	Cost Matrix
2	transformations	(undefined)	4.15	Evolutionary history
2	transformations	(undefined)	4.18	Gene duplication
2	transformations	(undefined)	4.19	Gene loss
2	transformations	(undefined)	4.20	Gene tree
2	transformations	(undefined)	4.21	Genetic event
2	transformations	(undefined)	4.28	Polarity
2	unclassified	(defined)	4.24	Distance Matrix
2	unclassified	(undefined)	4.12	Distance
3	methods	(defined)	4.16	Contrasts
3	methods	(defined)	4.25	Dollo Parsimony
3	methods	(defined)	4.32	General Time-Reversible Model (GTR)
3	methods	(defined)	4.46	Likelihood Method
3	methods	(defined)	4.54	Neighbor-Joining Algorithm
3	methods	(defined)	4.67	Parsimony Method
3	methods	(defined)	4.71	Phylogeny Inference Method
3	methods	(defined)	4.78	Reconcile Tree
3	methods	(defined)	4.91	Supertree
3	methods	(undefined)	4.22	Independent Contrasts Method
3	methods	(undefined)	4.23	Invariants
3	methods	(undefined)	4.26	minimum evolution
3	methods	(undefined)	4.4	Coalescent
3	methods	(undefined)	4.43	UPGMA
3	methods	(undefined)	4.6	Compatibility
3	methods	(undefined)	4.7	Consensus Tree
3	patterns	(defined)	4.36	Homoplasy
3	patterns	(defined)	4.37	Holophyly
3	patterns	(defined)	4.61	Orthology
3	patterns	(defined)	4.64	Parallel Evolution
3	patterns	(defined)	4.65	Paralogy
3	patterns	(defined)	4.66	Paraphyly
3	patterns	(defined)	4.72	Plesiomorphy
3	patterns	(defined)	4.74	Polyphyly
3	patterns	(defined)	4.92	Symplesiomorphy
3	patterns	(defined)	4.93	Synapomorphy
3	patterns	(undefined)	4.35	Reticulate Evolution
3	popgen	(defined)	4.1	Allele Fixation
3	popgen	(defined)	4.19	CpG Bias
3	popgen	(defined)	4.26	Drift
3	popgen	(defined)	4.29	Fixation
3	popgen	(defined)	4.51	Mutation
3	popgen	(defined)	4.52	Mutation Bias
3	popgen	(defined)	4.53	Natural Selection
3	popgen	(defined)	4.56	Neutral
3	popgen	(defined)	4.76	Random Genetic Drift
3	popgen	(defined)	4.84	Selection
3	popgen	(undefined)	4.30	Population
3	popgen	(undefined)	4.41	Transition-Transversion Bias
3	popgen	(undefined)	4.44	Variation
3	unclassified	(defined)	4.33	Genome Hypothesis
3	unclassified	(defined)	4.47	Molecular Clock
3	unclassified	(defined)	4.85	Silent
3	unclassified	(defined)	4.94	Synonymous
3	unclassified	(undefined)	4.1	Anagenesis
3	unclassified	(undefined)	4.11	Decay Index
3	unclassified	(undefined)	4.13	dN/dS
3	unclassified	(undefined)	4.14	Equilibrium State Frequencies
3	unclassified	(undefined)	4.17	GC/AT pressure
3	unclassified	(undefined)	4.24	Isochore
3	unclassified	(undefined)	4.3	Cladogenesis
3	unclassified	(undefined)	4.31	Positive Selection
3	unclassified	(undefined)	4.32	Radiation
3	unclassified	(undefined)	4.33	Radical
3	unclassified	(undefined)	4.34	Relative Rate Test
3	unclassified	(undefined)	4.36	Selective Constraint
3	unclassified	(undefined)	4.39	Stasis
3	unclassified	(undefined)	4.40	Star Tree
3	unclassified	(undefined)	4.45	Xenology
3	unclassified	(undefined)	4.5	Codon Usage
3	unclassified	(undefined)	4.8	Conservative
3	unclassified	(undefined)	4.9	Constraints, disambiguation