Contents
Index
elynx-tree-0.1.0: Handle phylogenetic trees
Index
adjacent
ELynx.Data.Tree.Distance
averageDistanceOriginLeaves
ELynx.Data.Tree.MeasurableTree
BDCD
ELynx.Distribution.BirthDeathCritical
bdcdLa
ELynx.Distribution.BirthDeathCritical
bdcdTOr
ELynx.Distribution.BirthDeathCritical
BDCNTD
ELynx.Distribution.BirthDeathCriticalNoTime
bdcntdLa
ELynx.Distribution.BirthDeathCriticalNoTime
BDD
ELynx.Distribution.BirthDeath
bddLa
ELynx.Distribution.BirthDeath
bddMu
ELynx.Distribution.BirthDeath
bddTOr
ELynx.Distribution.BirthDeath
BDNCD
ELynx.Distribution.BirthDeathNearlyCritical
bdncdLa
ELynx.Distribution.BirthDeathNearlyCritical
bdncdMu
ELynx.Distribution.BirthDeathNearlyCritical
bdncdTOr
ELynx.Distribution.BirthDeathNearlyCritical
bifurcating
ELynx.Data.Tree.Tree
Bipartition
ELynx.Data.Tree.Bipartition
bipartition
ELynx.Data.Tree.Bipartition
bipartitions
ELynx.Data.Tree.Bipartition
bipartitionToBranchLength
ELynx.Data.Tree.Bipartition
BirthDeathCriticalDistribution
ELynx.Distribution.BirthDeathCritical
BirthDeathCriticalNoTimeDistribution
ELynx.Distribution.BirthDeathCriticalNoTime
BirthDeathDistribution
ELynx.Distribution.BirthDeath
BirthDeathNearlyCriticalDistribution
ELynx.Distribution.BirthDeathNearlyCritical
bp
ELynx.Data.Tree.Bipartition
bphuman
ELynx.Data.Tree.Bipartition
bpmap
ELynx.Data.Tree.Bipartition
bps
ELynx.Data.Tree.Bipartition
branchLength
ELynx.Import.Tree.Newick
branchScore
ELynx.Data.Tree.Distance
branchScoreWith
ELynx.Data.Tree.Distance
BranchSupport
ELynx.Data.Tree.BranchSupportTree
BranchSupported
ELynx.Data.Tree.BranchSupportTree
brLen
ELynx.Data.Tree.PhyloTree
BrLnNChildren
ELynx.Data.Tree.SumStat
brSup
ELynx.Data.Tree.PhyloTree
clades
ELynx.Data.Tree.Tree
coalescentDistributionCont
ELynx.Distribution.CoalescentContinuous
collapse
ELynx.Data.Tree.BranchSupportTree
compatible
1 (Function)
ELynx.Data.Tree.Bipartition
2 (Function)
ELynx.Data.Tree.Multipartition
connect
ELynx.Data.Tree.Tree
cumulative
1 (Function)
ELynx.Distribution.TimeOfOriginNearCritical
2 (Function)
ELynx.Distribution.TimeOfOrigin
3 (Function)
ELynx.Distribution.BirthDeathNearlyCritical
4 (Function)
ELynx.Distribution.BirthDeathCriticalNoTime
5 (Function)
ELynx.Distribution.BirthDeathCritical
6 (Function)
ELynx.Distribution.BirthDeath
degree
ELynx.Data.Tree.Tree
density
1 (Function)
ELynx.Distribution.TimeOfOriginNearCritical
2 (Function)
ELynx.Distribution.TimeOfOrigin
3 (Function)
ELynx.Distribution.BirthDeathNearlyCritical
4 (Function)
ELynx.Distribution.BirthDeathCriticalNoTime
5 (Function)
ELynx.Distribution.BirthDeathCritical
6 (Function)
ELynx.Distribution.BirthDeath
distancesOriginLeaves
ELynx.Data.Tree.MeasurableTree
distancesRootLeaves
ELynx.Data.Tree.MeasurableTree
EvoLabel
ELynx.Data.Tree.EvoTree
extant
ELynx.Data.Tree.EvoTree
external
ELynx.Data.Tree.EvoTree
extinct
ELynx.Data.Tree.EvoTree
findSubset
ELynx.Data.Tree.Multipartition
forest
ELynx.Import.Tree.Newick
formatNChildSumStat
ELynx.Data.Tree.SumStat
fromBipartition
ELynx.Data.Tree.Multipartition
getBranchSupport
ELynx.Data.Tree.BranchSupportTree
getLen
ELynx.Data.Tree.MeasurableTree
getName
ELynx.Data.Tree.NamedTree
height
ELynx.Data.Tree.MeasurableTree
incompatibleSplits
ELynx.Data.Tree.Distance
incompatibleSplitsWith
ELynx.Data.Tree.Distance
internal
ELynx.Data.Tree.EvoTree
label
ELynx.Data.Tree.PhyloTree
leaf
ELynx.Import.Tree.Newick
leaves
ELynx.Data.Tree.Tree
lengthenStem
ELynx.Data.Tree.MeasurableTree
manyNewick
ELynx.Import.Tree.Newick
manyNewickIqTree
ELynx.Import.Tree.Newick
Measurable
ELynx.Data.Tree.MeasurableTree
merge
ELynx.Data.Tree.Tree
mp
ELynx.Data.Tree.Multipartition
mphuman
ELynx.Data.Tree.Multipartition
mpmap
ELynx.Data.Tree.Multipartition
mps
ELynx.Data.Tree.Multipartition
Multipartition
ELynx.Data.Tree.Multipartition
multipartitions
ELynx.Data.Tree.Multipartition
name
ELynx.Import.Tree.Newick
Named
ELynx.Data.Tree.NamedTree
NChildSumStat
ELynx.Data.Tree.SumStat
newick
ELynx.Import.Tree.Newick
newickIqTree
ELynx.Import.Tree.Newick
node
ELynx.Import.Tree.Newick
normalize
1 (Function)
ELynx.Data.Tree.BranchSupportTree
2 (Function)
ELynx.Data.Tree.MeasurableTree
nSubSamples
ELynx.Data.Tree.Tree
oneNewick
ELynx.Import.Tree.Newick
oneNewickIqTree
ELynx.Import.Tree.Newick
origin
ELynx.Simulate.PointProcess
pairwise
ELynx.Data.Tree.Distance
Parser
ELynx.Import.Tree.Newick
partitionTree
ELynx.Data.Tree.Tree
PhyloLabel
1 (Type/Class)
ELynx.Data.Tree.PhyloTree
2 (Data Constructor)
ELynx.Data.Tree.PhyloTree
PointProcess
1 (Type/Class)
ELynx.Simulate.PointProcess
2 (Data Constructor)
ELynx.Simulate.PointProcess
points
ELynx.Simulate.PointProcess
prune
ELynx.Data.Tree.MeasurableTree
pruneWith
ELynx.Data.Tree.Tree
quantile
1 (Function)
ELynx.Distribution.TimeOfOriginNearCritical
2 (Function)
ELynx.Distribution.TimeOfOrigin
3 (Function)
ELynx.Distribution.BirthDeathNearlyCritical
4 (Function)
ELynx.Distribution.BirthDeathCriticalNoTime
5 (Function)
ELynx.Distribution.BirthDeathCritical
6 (Function)
ELynx.Distribution.BirthDeath
Rate
ELynx.Distribution.Types
removeBrInfo
ELynx.Data.Tree.PhyloTree
removeMultifurcations
ELynx.Data.Tree.MeasurableTree
rootHeight
ELynx.Data.Tree.MeasurableTree
roots
ELynx.Data.Tree.Tree
sdifference
ELynx.Data.Tree.Subset
sdisjoint
ELynx.Data.Tree.Subset
sempty
ELynx.Data.Tree.Subset
setBranchSupport
ELynx.Data.Tree.BranchSupportTree
setLen
ELynx.Data.Tree.MeasurableTree
sfromlist
ELynx.Data.Tree.Subset
sfromset
ELynx.Data.Tree.Subset
shortenStem
ELynx.Data.Tree.MeasurableTree
simulate
1 (Function)
ELynx.Simulate.Coalescent
2 (Function)
ELynx.Simulate.PointProcess
simulateNReconstructedTrees
ELynx.Simulate.PointProcess
simulateReconstructedTree
ELynx.Simulate.PointProcess
singleton
ELynx.Data.Tree.Tree
sintersection
ELynx.Data.Tree.Subset
smap
ELynx.Data.Tree.Subset
smember
ELynx.Data.Tree.Subset
snull
ELynx.Data.Tree.Subset
sshow
ELynx.Data.Tree.Subset
ssingleton
ELynx.Data.Tree.Subset
subForestGetSubsets
ELynx.Data.Tree.Tree
subSample
ELynx.Data.Tree.Tree
Subset
ELynx.Data.Tree.Subset
subTree
ELynx.Data.Tree.Tree
summarize
ELynx.Data.Tree.MeasurableTree
sunion
ELynx.Data.Tree.Subset
sunions
ELynx.Data.Tree.Subset
symmetric
ELynx.Data.Tree.Distance
symmetricWith
ELynx.Data.Tree.Distance
Time
ELynx.Distribution.Types
TimeOfOriginDistribution
ELynx.Distribution.TimeOfOrigin
TimeOfOriginNearCriticalDistribution
ELynx.Distribution.TimeOfOriginNearCritical
TimeSpec
ELynx.Simulate.PointProcess
TOD
ELynx.Distribution.TimeOfOrigin
todLa
1 (Function)
ELynx.Distribution.TimeOfOriginNearCritical
2 (Function)
ELynx.Distribution.TimeOfOrigin
todMu
1 (Function)
ELynx.Distribution.TimeOfOriginNearCritical
2 (Function)
ELynx.Distribution.TimeOfOrigin
todTN
1 (Function)
ELynx.Distribution.TimeOfOriginNearCritical
2 (Function)
ELynx.Distribution.TimeOfOrigin
TONCD
ELynx.Distribution.TimeOfOriginNearCritical
toNChildSumStat
ELynx.Data.Tree.SumStat
toNewick
ELynx.Export.Tree.Newick
toReconstructedTree
ELynx.Simulate.PointProcess
totalBranchLength
ELynx.Data.Tree.MeasurableTree
tZipWith
ELynx.Data.Tree.Tree
ultrametric
ELynx.Data.Tree.MeasurableTree
values
ELynx.Simulate.PointProcess