| 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.Length, ELynx.Tree |
| coalescentDistributionCont | ELynx.Tree.Distribution.CoalescentContinuous |
| collapse | ELynx.Tree.Support, 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 |
| describeNewickFormat | ELynx.Tree.Import.Newick, ELynx.Tree |
| distancesOriginLeaves | ELynx.Tree.Length, 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 | |
| 1 (Function) | ELynx.Topology.Phylogeny, ELynx.Topology |
| 2 (Function) | ELynx.Tree.Phylogeny, ELynx.Tree |
| equal' | |
| 1 (Function) | ELynx.Topology.Phylogeny, ELynx.Topology |
| 2 (Function) | ELynx.Tree.Phylogeny, ELynx.Tree |
| 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.Length, ELynx.Tree |
| fromName | ELynx.Tree.Name, ELynx.Tree |
| fromPartition | ELynx.Tree.Partition, ELynx.Tree |
| fromSupport | ELynx.Tree.Support, 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.Length, ELynx.Tree |
| getName | ELynx.Tree.Name, ELynx.Tree |
| getSubTreeUnsafe | ELynx.Tree.Zipper, ELynx.Tree |
| getSup | ELynx.Tree.Support, ELynx.Tree |
| goChild | ELynx.Tree.Zipper, ELynx.Tree |
| goChildUnsafe | ELynx.Tree.Zipper, ELynx.Tree |
| goLeft | ELynx.Tree.Zipper, ELynx.Tree |
| goParent | ELynx.Tree.Zipper, ELynx.Tree |
| goParentUnsafe | 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 |
| groups | ELynx.Tree.Bipartition, ELynx.Tree |
| HasLength | ELynx.Tree.Length, ELynx.Tree |
| HasName | ELynx.Tree.Name, ELynx.Tree |
| HasSupport | ELynx.Tree.Support, ELynx.Tree |
| height | ELynx.Tree.Length, 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.Length, ELynx.Tree |
| makeUltrametric | ELynx.Tree.Length, ELynx.Tree |
| measurableToPhyloTree | ELynx.Tree.Phylogeny, ELynx.Tree |
| midpoint | ELynx.Tree.Phylogeny, ELynx.Tree |
| modifyTree | ELynx.Tree.Zipper, ELynx.Tree |
| modLen | ELynx.Tree.Length, ELynx.Tree |
| modSup | ELynx.Tree.Support, ELynx.Tree |
| Mrca | ELynx.Tree.Simulate.PointProcess |
| Name | |
| 1 (Type/Class) | ELynx.Tree.Name, ELynx.Tree |
| 2 (Data Constructor) | ELynx.Tree.Name, 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.Length, ELynx.Tree |
| normalizeBranchSupport | ELynx.Tree.Support, ELynx.Tree |
| normalizeHeight | ELynx.Tree.Length, ELynx.Tree |
| oneNewick | ELynx.Tree.Import.Newick, ELynx.Tree |
| Origin | ELynx.Tree.Simulate.PointProcess |
| origin | ELynx.Tree.Simulate.PointProcess |
| outgroup | 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 |
| rootHeight | ELynx.Tree.Length, ELynx.Tree |
| roots | 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.Length, ELynx.Tree |
| setStem | ELynx.Tree.Rooted, ELynx.Tree |
| setSup | ELynx.Tree.Support, 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.Support, 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.Length, ELynx.Tree |
| toLengthUnsafe | ELynx.Tree.Length, 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.Support, ELynx.Tree |
| toSupportUnsafe | ELynx.Tree.Support, ELynx.Tree |
| totalBranchLength | ELynx.Tree.Length, 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.Length, ELynx.Tree |
| validPath | ELynx.Tree.Zipper, 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 |