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Binary Tree:
- A tree in which every internal node has
degree three. If the tree is rooted, every internal node has
one parent and two children. Also known as a
Bifurcating Tree.
- Bipartition:
- In the phylogenetic context, the separation of
the leaf taxa into two sets. Each edge in the tree specifies
the taxon bipartition that would result if the edge were
removed. Also called a Split.
- Combined Loss:
- The interpretation that the absence of a gene
in two or more sibling species is evidence of a single loss
in their common ancestor.
- Conditional Duplication:
- In a gene tree reconciled with a
non-binary species tree, a node whose incongruence with the
species tree could be due to either deep coalescence or
duplication.
- Conditional Duplication Cost:
- The weight cC of each conditional duplication in the D/L Score. By
default, cC = 0.
- Duplication/Loss Score:
- The weighted sum, cL L + cD D +
cC C , of losses (L),
duplications (D) and conditional duplications (C) in a
reconciled gene tree. Also known as the D/L Score or the
D/L cost.
- Deep Coalescence:
- The divergence of genes when the time of
separation of a gene lineage predates the time
of speciation.
- Duplication Cost:
- The weight cD
of each duplication in the D/L Score. By default,
cD = 1.5
- Edge Weight:
- A numerical value representing a quantitative
assessment of the support in the underlying data for the
associated bipartition. Typically bootstrap values, branch
lengths, or likelihood scores are used as edge weights. If
used, edge weights are specified in the input gene tree file.
- Edge Weight Threshold:
- Numerical value used to define strong
edges. Edges with weights below the edge weight threshold
are considered unreliable or weak.
- Event History:
- A set of event-edge pairs, where each event
is a duplication or a loss and each edge is an edge in the
species tree that specifies when the event occurred. An
event history specifies a set of trees in which any tree in
the set can be obtained from any other tree in the set by a
series of Same Cost Swaps.
- Hard Polytomy:
- A polytomy that represents the simultaneous
divergence of the three or more lineages. Hard polytomies
are only found in species trees. See also Soft Polytomy.
- Height:
- The maximum path length between any leaf and the
root of a tree.
- Incomplete Lineage Sorting:
- Incongruence between a gene and
species tree that occurs when the lineages of a gene tree
sort independently from the lineages of the associated
species tree.
- Loss Cost:
- The weight cL of
each loss in the D/L Score. By default, cL = 1.0
- Non-binary Tree:
- A tree in which at least one node has
degree greater than three. In a rooted non-binary tree, at
least one node has more than two children. Also known as a
Multifurcating Tree.
- Polytomy:
- A node with degree greater than three. In a
rooted tree, a node with more than two children.
- Polytomy Size:
- The number of children of a polytomy in a
rooted tree.
- Pruned Species Tree:
- A species tree containing only the
species that appear in the gene tree with which it was
reconciled.
- Rearranged Tree:
- A reconciled, binary gene tree with minimal
D/L Score that agrees with the original tree at all strongly
supported edges.
- Reconciled Tree:
- A gene tree that has been fit to a species
tree, resulting in a mapping between each node in the gene
tree and a node in the species tree. From this mapping, gene
losses and duplications are inferred.
- Required Duplication:
- In a gene tree reconciled with a
non-binary species tree, a node whose incongruence with the
species tree can only be explained by a duplication.
- Resolved Tree:
- A binary tree derived from a non-binary
gene tree, in which each polytomy has
been removed and replaced with a set of binary divergences.
- Same Cost Swap:
- An interchange of two nodes in the gene tree
that does not change the D/L Score of the tree, and does not
break any Strong Edges.
- Soft Polytomy:
- A polytomy that represents uncertainty in
the true, binary branching pattern of its descendant
lineages. Soft polytomies can be found in either gene or
species trees.
- Strong Edge:
- An edge with weight greater than or equal to
the Edge Weight Threshold. Any edge without a
specified weight is assumed to be weak.
- Trifurcation:
- In a rooted tree, a node with exactly three
children.
- Weak Edge:
- An edge with weight lower than the Edge
Weight Threshold. Any edge without a specified weight is
assumed to be weak.