after | ELynx.Tree.Zipper, ELynx.Tree |
applyLabel | ELynx.Tree.Rooted, ELynx.Tree |
applyRoot | ELynx.Tree.Rooted, ELynx.Tree |
applyStem | ELynx.Tree.Rooted, ELynx.Tree |
BDCD | ELynx.Tree.Distribution.BirthDeathCritical |
bdcdLa | ELynx.Tree.Distribution.BirthDeathCritical |
bdcdTOr | ELynx.Tree.Distribution.BirthDeathCritical |
BDCNTD | ELynx.Tree.Distribution.BirthDeathCriticalNoTime |
bdcntdLa | ELynx.Tree.Distribution.BirthDeathCriticalNoTime |
BDD | ELynx.Tree.Distribution.BirthDeath |
bddLa | ELynx.Tree.Distribution.BirthDeath |
bddMu | ELynx.Tree.Distribution.BirthDeath |
bddTOr | ELynx.Tree.Distribution.BirthDeath |
BDNCD | ELynx.Tree.Distribution.BirthDeathNearlyCritical |
bdncdLa | ELynx.Tree.Distribution.BirthDeathNearlyCritical |
bdncdMu | ELynx.Tree.Distribution.BirthDeathNearlyCritical |
bdncdTOr | ELynx.Tree.Distribution.BirthDeathNearlyCritical |
before | ELynx.Tree.Zipper, ELynx.Tree |
bifurcating | ELynx.Tree.Phylogeny, ELynx.Tree |
Bipartition | ELynx.Tree.Bipartition, ELynx.Tree |
bipartition | ELynx.Tree.Bipartition, ELynx.Tree |
bipartitions | ELynx.Tree.Bipartition, ELynx.Tree |
bipartitionToBranch | ELynx.Tree.Bipartition, ELynx.Tree |
BirthDeathCriticalDistribution | ELynx.Tree.Distribution.BirthDeathCritical |
BirthDeathCriticalNoTimeDistribution | ELynx.Tree.Distribution.BirthDeathCriticalNoTime |
BirthDeathDistribution | ELynx.Tree.Distribution.BirthDeath |
BirthDeathNearlyCriticalDistribution | ELynx.Tree.Distribution.BirthDeathNearlyCritical |
bp | ELynx.Tree.Bipartition, ELynx.Tree |
bpHuman | ELynx.Tree.Bipartition, ELynx.Tree |
bpToPt | ELynx.Tree.Partition, ELynx.Tree |
bpUnsafe | ELynx.Tree.Bipartition, ELynx.Tree |
branch | ELynx.Tree.Rooted, ELynx.Tree |
branches | ELynx.Tree.Rooted, ELynx.Tree |
branchScore | ELynx.Tree.Distance, ELynx.Tree |
brLen | ELynx.Tree.Phylogeny, ELynx.Tree |
brSup | ELynx.Tree.Phylogeny, ELynx.Tree |
checkLength | ELynx.Tree.Measurable, ELynx.Tree |
coalescentDistributionCont | ELynx.Tree.Distribution.CoalescentContinuous |
collapse | ELynx.Tree.Supported, ELynx.Tree |
compatible | ELynx.Tree.Partition, ELynx.Tree |
cumulative | |
1 (Function) | ELynx.Tree.Distribution.TimeOfOriginNearCritical |
2 (Function) | ELynx.Tree.Distribution.TimeOfOrigin |
3 (Function) | ELynx.Tree.Distribution.BirthDeathNearlyCritical |
4 (Function) | ELynx.Tree.Distribution.BirthDeathCriticalNoTime |
5 (Function) | ELynx.Tree.Distribution.BirthDeathCritical |
6 (Function) | ELynx.Tree.Distribution.BirthDeath |
current | ELynx.Tree.Zipper, ELynx.Tree |
degree | |
1 (Function) | ELynx.Tree.Rooted, ELynx.Tree |
2 (Function) | ELynx.Topology.Rooted, ELynx.Topology |
density | |
1 (Function) | ELynx.Tree.Distribution.TimeOfOriginNearCritical |
2 (Function) | ELynx.Tree.Distribution.TimeOfOrigin |
3 (Function) | ELynx.Tree.Distribution.BirthDeathNearlyCritical |
4 (Function) | ELynx.Tree.Distribution.BirthDeathCriticalNoTime |
5 (Function) | ELynx.Tree.Distribution.BirthDeathCritical |
6 (Function) | ELynx.Tree.Distribution.BirthDeath |
description | ELynx.Tree.Import.Newick, ELynx.Tree |
distancesOriginLeaves | ELynx.Tree.Measurable, ELynx.Tree |
dropLeavesWith | |
1 (Function) | ELynx.Tree.Rooted, ELynx.Tree |
2 (Function) | ELynx.Topology.Rooted, ELynx.Topology |
dropNodesWith | ELynx.Tree.Rooted, ELynx.Tree |
duplicateLeaves | |
1 (Function) | ELynx.Tree.Rooted, ELynx.Tree |
2 (Function) | ELynx.Topology.Rooted, ELynx.Topology |
equal | ELynx.Tree.Phylogeny, ELynx.Tree |
flatten | ELynx.Topology.Rooted, ELynx.Topology |
Forest | |
1 (Type/Class) | ELynx.Tree.Rooted, ELynx.Tree |
2 (Type/Class) | ELynx.Topology.Rooted, ELynx.Topology |
forest | |
1 (Function) | ELynx.Tree.Rooted, ELynx.Tree |
2 (Function) | ELynx.Topology.Rooted, ELynx.Topology |
fromBipartition | ELynx.Tree.Bipartition, ELynx.Tree |
fromLabeledTree | ELynx.Topology.Rooted, ELynx.Topology |
fromLength | ELynx.Tree.Measurable, ELynx.Tree |
fromName | ELynx.Tree.Named, ELynx.Tree |
fromPartition | ELynx.Tree.Partition, ELynx.Tree |
fromSupport | ELynx.Tree.Supported, ELynx.Tree |
fromTree | |
1 (Function) | ELynx.Topology.Rooted, ELynx.Topology |
2 (Function) | ELynx.Tree.Zipper, ELynx.Tree |
getComplementaryLeaves | ELynx.Tree.Bipartition, ELynx.Tree |
getLen | ELynx.Tree.Measurable, ELynx.Tree |
getName | ELynx.Tree.Named, ELynx.Tree |
getSubTreeUnsafe | ELynx.Tree.Zipper, ELynx.Tree |
getSup | ELynx.Tree.Supported, ELynx.Tree |
goChild | ELynx.Tree.Zipper, ELynx.Tree |
goLeft | ELynx.Tree.Zipper, ELynx.Tree |
goPath | ELynx.Tree.Zipper, ELynx.Tree |
goPathUnsafe | ELynx.Tree.Zipper, ELynx.Tree |
goRight | ELynx.Tree.Zipper, ELynx.Tree |
goRoot | ELynx.Tree.Zipper, ELynx.Tree |
goUp | ELynx.Tree.Zipper, ELynx.Tree |
groups | ELynx.Tree.Bipartition, ELynx.Tree |
height | ELynx.Tree.Measurable, ELynx.Tree |
identify | |
1 (Function) | ELynx.Tree.Rooted, ELynx.Tree |
2 (Function) | ELynx.Topology.Rooted, ELynx.Topology |
incompatibleSplits | ELynx.Tree.Distance, ELynx.Tree |
insertBranch | ELynx.Tree.Zipper, ELynx.Tree |
insertLabel | ELynx.Tree.Zipper, ELynx.Tree |
insertTree | ELynx.Tree.Zipper, ELynx.Tree |
intersect | ELynx.Tree.Phylogeny, ELynx.Tree |
IqTree | ELynx.Tree.Import.Newick, ELynx.Tree |
label | |
1 (Function) | ELynx.Tree.Rooted, ELynx.Tree |
2 (Function) | ELynx.Topology.Rooted, ELynx.Topology |
labels | ELynx.Tree.Rooted, ELynx.Tree |
Leaf | ELynx.Topology.Rooted, ELynx.Topology |
leaves | |
1 (Function) | ELynx.Tree.Rooted, ELynx.Tree |
2 (Function) | ELynx.Topology.Rooted, ELynx.Topology |
Length | ELynx.Tree.Measurable, ELynx.Tree |
makeUltrametric | ELynx.Tree.Measurable, ELynx.Tree |
Measurable | ELynx.Tree.Measurable, ELynx.Tree |
measurableToPhyloTree | ELynx.Tree.Phylogeny, ELynx.Tree |
midpoint | ELynx.Tree.Phylogeny, ELynx.Tree |
modLen | ELynx.Tree.Measurable, ELynx.Tree |
modSup | ELynx.Tree.Supported, ELynx.Tree |
Mrca | ELynx.Tree.Simulate.PointProcess |
Name | |
1 (Type/Class) | ELynx.Tree.Named, ELynx.Tree |
2 (Data Constructor) | ELynx.Tree.Named, ELynx.Tree |
Named | ELynx.Tree.Named, ELynx.Tree |
newick | ELynx.Tree.Import.Newick, ELynx.Tree |
NewickFormat | ELynx.Tree.Import.Newick, ELynx.Tree |
nexusTrees | ELynx.Tree.Import.Nexus, ELynx.Tree |
Node | |
1 (Data Constructor) | ELynx.Tree.Rooted, ELynx.Tree |
2 (Data Constructor) | ELynx.Topology.Rooted, ELynx.Topology |
normalizeBranchLengths | ELynx.Tree.Measurable, ELynx.Tree |
normalizeBranchSupport | ELynx.Tree.Supported, ELynx.Tree |
normalizeHeight | ELynx.Tree.Measurable, ELynx.Tree |
oneNewick | ELynx.Tree.Import.Newick, ELynx.Tree |
Origin | ELynx.Tree.Simulate.PointProcess |
origin | ELynx.Tree.Simulate.PointProcess |
outgroup | |
1 (Function) | ELynx.Topology.Phylogeny, ELynx.Topology |
2 (Function) | ELynx.Tree.Phylogeny, ELynx.Tree |
parBranchFoldMap | ELynx.Tree.Parallel, ELynx.Tree |
parents | ELynx.Tree.Zipper, ELynx.Tree |
parNodeFoldMap | ELynx.Tree.Parallel, ELynx.Tree |
parseNewick | ELynx.Tree.Import.Newick, ELynx.Tree |
parseOneNewick | ELynx.Tree.Import.Newick, ELynx.Tree |
parseSomeNewick | ELynx.Tree.Import.Newick, ELynx.Tree |
Partition | ELynx.Tree.Partition, ELynx.Tree |
partition | ELynx.Tree.Partition, ELynx.Tree |
partitions | ELynx.Tree.Partition, ELynx.Tree |
parTree | ELynx.Tree.Parallel, ELynx.Tree |
Path | ELynx.Tree.Zipper, ELynx.Tree |
Phylo | |
1 (Type/Class) | ELynx.Tree.Phylogeny, ELynx.Tree |
2 (Data Constructor) | ELynx.Tree.Phylogeny, ELynx.Tree |
PhyloExplicit | |
1 (Type/Class) | ELynx.Tree.Phylogeny, ELynx.Tree |
2 (Data Constructor) | ELynx.Tree.Phylogeny, ELynx.Tree |
phyloToLengthTree | ELynx.Tree.Phylogeny, ELynx.Tree |
phyloToSupportTree | ELynx.Tree.Phylogeny, ELynx.Tree |
phyloToSupportTreeUnsafe | ELynx.Tree.Phylogeny, ELynx.Tree |
PointProcess | |
1 (Type/Class) | ELynx.Tree.Simulate.PointProcess |
2 (Data Constructor) | ELynx.Tree.Simulate.PointProcess |
points | ELynx.Tree.Simulate.PointProcess |
Pos | ELynx.Tree.Zipper, ELynx.Tree |
prune | |
1 (Function) | ELynx.Tree.Rooted, ELynx.Tree |
2 (Function) | ELynx.Topology.Rooted, ELynx.Topology |
pt | ELynx.Tree.Partition, ELynx.Tree |
ptHuman | ELynx.Tree.Partition, ELynx.Tree |
ptUnsafe | ELynx.Tree.Partition, ELynx.Tree |
quantile | |
1 (Function) | ELynx.Tree.Distribution.TimeOfOriginNearCritical |
2 (Function) | ELynx.Tree.Distribution.TimeOfOrigin |
3 (Function) | ELynx.Tree.Distribution.BirthDeathNearlyCritical |
4 (Function) | ELynx.Tree.Distribution.BirthDeathCriticalNoTime |
5 (Function) | ELynx.Tree.Distribution.BirthDeathCritical |
6 (Function) | ELynx.Tree.Distribution.BirthDeath |
Random | ELynx.Tree.Simulate.PointProcess |
Rate | ELynx.Tree.Distribution.Types |
RevBayes | ELynx.Tree.Import.Newick, ELynx.Tree |
rootAt | |
1 (Function) | ELynx.Topology.Phylogeny, ELynx.Topology |
2 (Function) | ELynx.Tree.Phylogeny, ELynx.Tree |
rootHeight | ELynx.Tree.Measurable, ELynx.Tree |
roots | |
1 (Function) | ELynx.Topology.Phylogeny, ELynx.Topology |
2 (Function) | ELynx.Tree.Phylogeny, ELynx.Tree |
sBrLen | ELynx.Tree.Phylogeny, ELynx.Tree |
sBrSup | ELynx.Tree.Phylogeny, ELynx.Tree |
setBranches | ELynx.Tree.Rooted, ELynx.Tree |
setLabel | ELynx.Tree.Rooted, ELynx.Tree |
setLabels | ELynx.Tree.Rooted, ELynx.Tree |
setLen | ELynx.Tree.Measurable, ELynx.Tree |
setStem | ELynx.Tree.Rooted, ELynx.Tree |
setSup | ELynx.Tree.Supported, ELynx.Tree |
simulate | |
1 (Function) | ELynx.Tree.Simulate.PointProcess |
2 (Function) | ELynx.Tree.Simulate.Coalescent |
simulateNReconstructedTrees | ELynx.Tree.Simulate.PointProcess |
simulateReconstructedTree | ELynx.Tree.Simulate.PointProcess |
someNewick | ELynx.Tree.Import.Newick, ELynx.Tree |
split | ELynx.Tree.Splittable, ELynx.Tree |
Splittable | ELynx.Tree.Splittable, ELynx.Tree |
Standard | ELynx.Tree.Import.Newick, ELynx.Tree |
Support | ELynx.Tree.Supported, ELynx.Tree |
Supported | ELynx.Tree.Supported, ELynx.Tree |
supportedToPhyloTree | ELynx.Tree.Phylogeny, ELynx.Tree |
symmetric | ELynx.Tree.Distance, ELynx.Tree |
Time | ELynx.Tree.Distribution.Types |
TimeOfOriginDistribution | ELynx.Tree.Distribution.TimeOfOrigin |
TimeOfOriginNearCriticalDistribution | ELynx.Tree.Distribution.TimeOfOriginNearCritical |
TimeSpec | ELynx.Tree.Simulate.PointProcess |
TOD | ELynx.Tree.Distribution.TimeOfOrigin |
todLa | |
1 (Function) | ELynx.Tree.Distribution.TimeOfOriginNearCritical |
2 (Function) | ELynx.Tree.Distribution.TimeOfOrigin |
todMu | |
1 (Function) | ELynx.Tree.Distribution.TimeOfOriginNearCritical |
2 (Function) | ELynx.Tree.Distribution.TimeOfOrigin |
todTN | |
1 (Function) | ELynx.Tree.Distribution.TimeOfOriginNearCritical |
2 (Function) | ELynx.Tree.Distribution.TimeOfOrigin |
toExplicitTree | ELynx.Tree.Phylogeny, ELynx.Tree |
toLength | ELynx.Tree.Measurable, ELynx.Tree |
toLengthUnsafe | ELynx.Tree.Measurable, ELynx.Tree |
TONCD | ELynx.Tree.Distribution.TimeOfOriginNearCritical |
toNewick | ELynx.Tree.Export.Newick, ELynx.Tree |
toNewickBuilder | ELynx.Tree.Export.Newick, ELynx.Tree |
toNexusTrees | ELynx.Tree.Export.Nexus, ELynx.Tree |
toPhyloTree | ELynx.Tree.Phylogeny, ELynx.Tree |
Topology | ELynx.Topology.Rooted, ELynx.Topology |
toReconstructedTree | ELynx.Tree.Simulate.PointProcess |
toSet | ELynx.Tree.Bipartition, ELynx.Tree |
toSupport | ELynx.Tree.Supported, ELynx.Tree |
toSupportUnsafe | ELynx.Tree.Supported, ELynx.Tree |
totalBranchLength | ELynx.Tree.Measurable, ELynx.Tree |
toTree | ELynx.Tree.Zipper, ELynx.Tree |
toTreeBranchLabels | ELynx.Tree.Rooted, ELynx.Tree |
toTreeNodeLabels | ELynx.Tree.Rooted, ELynx.Tree |
Tree | ELynx.Tree.Rooted, ELynx.Tree |
TreePos | ELynx.Tree.Zipper, ELynx.Tree |
ultrametric | ELynx.Tree.Measurable, ELynx.Tree |
values | ELynx.Tree.Simulate.PointProcess |
zipTrees | |
1 (Function) | ELynx.Tree.Rooted, ELynx.Tree |
2 (Function) | ELynx.Topology.Rooted, ELynx.Topology |
zipTreesWith | |
1 (Function) | ELynx.Tree.Rooted, ELynx.Tree |
2 (Function) | ELynx.Topology.Rooted, ELynx.Topology |