| after | ELynx.Data.Tree.Zipper, ELynx.Data.Tree |
| applyStem | ELynx.Data.Tree.Measurable, ELynx.Data.Tree |
| 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 |
| before | ELynx.Data.Tree.Zipper, ELynx.Data.Tree |
| bifurcating | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| Bipartition | ELynx.Data.Tree.Bipartition, ELynx.Data.Tree |
| bipartition | ELynx.Data.Tree.Bipartition, ELynx.Data.Tree |
| bipartitions | ELynx.Data.Tree.Bipartition, ELynx.Data.Tree |
| bipartitionToBranch | ELynx.Data.Tree.Bipartition, ELynx.Data.Tree |
| BirthDeathCriticalDistribution | ELynx.Distribution.BirthDeathCritical |
| BirthDeathCriticalNoTimeDistribution | ELynx.Distribution.BirthDeathCriticalNoTime |
| BirthDeathDistribution | ELynx.Distribution.BirthDeath |
| BirthDeathNearlyCriticalDistribution | ELynx.Distribution.BirthDeathNearlyCritical |
| bp | ELynx.Data.Tree.Bipartition, ELynx.Data.Tree |
| bpHuman | ELynx.Data.Tree.Bipartition, ELynx.Data.Tree |
| bpToMp | ELynx.Data.Tree.Partition, ELynx.Data.Tree |
| bpUnsafe | ELynx.Data.Tree.Bipartition, ELynx.Data.Tree |
| branch | ELynx.Data.Tree.Rooted, ELynx.Data.Tree |
| branches | ELynx.Data.Tree.Rooted, ELynx.Data.Tree |
| BranchLength | ELynx.Data.Tree.Measurable, ELynx.Data.Tree |
| branchScore | ELynx.Data.Tree.Distance, ELynx.Data.Tree |
| BranchSupport | ELynx.Data.Tree.Supported, ELynx.Data.Tree |
| brLen | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| brSup | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| coalescentDistributionCont | ELynx.Distribution.CoalescentContinuous |
| collapse | ELynx.Data.Tree.Supported, ELynx.Data.Tree |
| compatible | ELynx.Data.Tree.Partition, ELynx.Data.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 |
| current | ELynx.Data.Tree.Zipper, ELynx.Data.Tree |
| degree | |
| 1 (Function) | ELynx.Data.Tree.Rooted, ELynx.Data.Tree |
| 2 (Function) | ELynx.Data.Topology.Rooted |
| 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 |
| description | ELynx.Import.Tree.Newick |
| distancesOriginLeaves | ELynx.Data.Tree.Measurable, ELynx.Data.Tree |
| dropLeavesWith | |
| 1 (Function) | ELynx.Data.Tree.Rooted, ELynx.Data.Tree |
| 2 (Function) | ELynx.Data.Topology.Rooted |
| dropNodesWith | ELynx.Data.Tree.Rooted, ELynx.Data.Tree |
| duplicateLeaves | |
| 1 (Function) | ELynx.Data.Tree.Rooted, ELynx.Data.Tree |
| 2 (Function) | ELynx.Data.Topology.Rooted |
| equal | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| flatten | ELynx.Data.Topology.Rooted |
| Forest | |
| 1 (Type/Class) | ELynx.Data.Tree.Rooted, ELynx.Data.Tree |
| 2 (Type/Class) | ELynx.Data.Topology.Rooted |
| forest | |
| 1 (Function) | ELynx.Data.Tree.Rooted, ELynx.Data.Tree |
| 2 (Function) | ELynx.Data.Topology.Rooted |
| fromBipartition | ELynx.Data.Tree.Bipartition, ELynx.Data.Tree |
| fromLabeledTree | ELynx.Data.Topology.Rooted |
| fromLength | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| fromPartition | ELynx.Data.Tree.Partition, ELynx.Data.Tree |
| fromSupport | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| fromTree | |
| 1 (Function) | ELynx.Data.Topology.Rooted |
| 2 (Function) | ELynx.Data.Tree.Zipper, ELynx.Data.Tree |
| getComplementaryLeaves | ELynx.Data.Tree.Bipartition, ELynx.Data.Tree |
| getLen | ELynx.Data.Tree.Measurable, ELynx.Data.Tree |
| getName | ELynx.Data.Tree.Named, ELynx.Data.Tree |
| getStem | ELynx.Data.Tree.Measurable, ELynx.Data.Tree |
| getSup | ELynx.Data.Tree.Supported, ELynx.Data.Tree |
| goChild | ELynx.Data.Tree.Zipper, ELynx.Data.Tree |
| goLeft | ELynx.Data.Tree.Zipper, ELynx.Data.Tree |
| goPath | ELynx.Data.Tree.Zipper, ELynx.Data.Tree |
| goRight | ELynx.Data.Tree.Zipper, ELynx.Data.Tree |
| goRoot | ELynx.Data.Tree.Zipper, ELynx.Data.Tree |
| goUp | ELynx.Data.Tree.Zipper, ELynx.Data.Tree |
| groups | ELynx.Data.Tree.Bipartition, ELynx.Data.Tree |
| height | ELynx.Data.Tree.Measurable, ELynx.Data.Tree |
| identify | |
| 1 (Function) | ELynx.Data.Tree.Rooted, ELynx.Data.Tree |
| 2 (Function) | ELynx.Data.Topology.Rooted |
| incompatibleSplits | ELynx.Data.Tree.Distance, ELynx.Data.Tree |
| insertBranch | ELynx.Data.Tree.Zipper, ELynx.Data.Tree |
| insertLabel | ELynx.Data.Tree.Zipper, ELynx.Data.Tree |
| insertTree | ELynx.Data.Tree.Zipper, ELynx.Data.Tree |
| intersect | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| IqTree | ELynx.Import.Tree.Newick |
| label | |
| 1 (Function) | ELynx.Data.Tree.Rooted, ELynx.Data.Tree |
| 2 (Function) | ELynx.Data.Topology.Rooted |
| labels | ELynx.Data.Tree.Rooted, ELynx.Data.Tree |
| Leaf | ELynx.Data.Topology.Rooted |
| leaves | |
| 1 (Function) | ELynx.Data.Tree.Rooted, ELynx.Data.Tree |
| 2 (Function) | ELynx.Data.Topology.Rooted |
| Length | |
| 1 (Type/Class) | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| 2 (Data Constructor) | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| makeUltrametric | ELynx.Data.Tree.Measurable, ELynx.Data.Tree |
| Measurable | ELynx.Data.Tree.Measurable, ELynx.Data.Tree |
| measurableToPhyloTree | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| midpoint | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| mp | ELynx.Data.Tree.Partition, ELynx.Data.Tree |
| mpHuman | ELynx.Data.Tree.Partition, ELynx.Data.Tree |
| mpUnsafe | ELynx.Data.Tree.Partition, ELynx.Data.Tree |
| Named | ELynx.Data.Tree.Named, ELynx.Data.Tree |
| newick | ELynx.Import.Tree.Newick |
| NewickFormat | ELynx.Import.Tree.Newick |
| nexusTrees | ELynx.Import.Tree.Nexus |
| Node | |
| 1 (Data Constructor) | ELynx.Data.Tree.Rooted, ELynx.Data.Tree |
| 2 (Data Constructor) | ELynx.Data.Topology.Rooted |
| normalizeBranchLengths | ELynx.Data.Tree.Measurable, ELynx.Data.Tree |
| normalizeBranchSupport | ELynx.Data.Tree.Supported, ELynx.Data.Tree |
| normalizeHeight | ELynx.Data.Tree.Measurable, ELynx.Data.Tree |
| oneNewick | ELynx.Import.Tree.Newick |
| origin | ELynx.Simulate.PointProcess |
| outgroup | |
| 1 (Function) | ELynx.Data.Topology.Phylogeny |
| 2 (Function) | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| parents | ELynx.Data.Tree.Zipper, ELynx.Data.Tree |
| Partition | ELynx.Data.Tree.Partition, ELynx.Data.Tree |
| partition | ELynx.Data.Tree.Partition, ELynx.Data.Tree |
| partitions | ELynx.Data.Tree.Partition, ELynx.Data.Tree |
| Phylo | |
| 1 (Type/Class) | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| 2 (Data Constructor) | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| PhyloExplicit | |
| 1 (Type/Class) | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| 2 (Data Constructor) | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| phyloToLengthTree | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| phyloToSupportTree | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| phyloToSupportTreeUnsafe | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| PointProcess | |
| 1 (Type/Class) | ELynx.Simulate.PointProcess |
| 2 (Data Constructor) | ELynx.Simulate.PointProcess |
| points | ELynx.Simulate.PointProcess |
| Pos | ELynx.Data.Tree.Zipper, ELynx.Data.Tree |
| prune | |
| 1 (Function) | ELynx.Data.Tree.Rooted, ELynx.Data.Tree |
| 2 (Function) | ELynx.Data.Topology.Rooted |
| 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 |
| RevBayes | ELynx.Import.Tree.Newick |
| rootAt | |
| 1 (Function) | ELynx.Data.Topology.Phylogeny |
| 2 (Function) | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| rootHeight | ELynx.Data.Tree.Measurable, ELynx.Data.Tree |
| roots | |
| 1 (Function) | ELynx.Data.Topology.Phylogeny |
| 2 (Function) | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| sBrLen | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| sBrSup | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| setBranches | ELynx.Data.Tree.Rooted, ELynx.Data.Tree |
| setLabels | ELynx.Data.Tree.Rooted, ELynx.Data.Tree |
| setLen | ELynx.Data.Tree.Measurable, ELynx.Data.Tree |
| setStem | ELynx.Data.Tree.Measurable, ELynx.Data.Tree |
| setSup | ELynx.Data.Tree.Supported, ELynx.Data.Tree |
| simulate | |
| 1 (Function) | ELynx.Simulate.Coalescent |
| 2 (Function) | ELynx.Simulate.PointProcess |
| simulateNReconstructedTrees | ELynx.Simulate.PointProcess |
| simulateReconstructedTree | ELynx.Simulate.PointProcess |
| someNewick | ELynx.Import.Tree.Newick |
| split | ELynx.Data.Tree.Splittable, ELynx.Data.Tree |
| Splittable | ELynx.Data.Tree.Splittable, ELynx.Data.Tree |
| Standard | ELynx.Import.Tree.Newick |
| Support | |
| 1 (Type/Class) | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| 2 (Data Constructor) | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| Supported | ELynx.Data.Tree.Supported, ELynx.Data.Tree |
| supportedToPhyloTree | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| symmetric | ELynx.Data.Tree.Distance, ELynx.Data.Tree |
| 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 |
| toExplicitTree | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| TONCD | ELynx.Distribution.TimeOfOriginNearCritical |
| toNewick | ELynx.Export.Tree.Newick |
| toNewickBuilder | ELynx.Export.Tree.Newick |
| toNexusTrees | ELynx.Export.Tree.Nexus |
| toPhyloTree | ELynx.Data.Tree.Phylogeny, ELynx.Data.Tree |
| Topology | ELynx.Data.Topology.Rooted |
| toReconstructedTree | ELynx.Simulate.PointProcess |
| toSet | ELynx.Data.Tree.Bipartition, ELynx.Data.Tree |
| totalBranchLength | ELynx.Data.Tree.Measurable, ELynx.Data.Tree |
| toTree | ELynx.Data.Tree.Zipper, ELynx.Data.Tree |
| toTreeBranchLabels | ELynx.Data.Tree.Rooted, ELynx.Data.Tree |
| toTreeNodeLabels | ELynx.Data.Tree.Rooted, ELynx.Data.Tree |
| Tree | ELynx.Data.Tree.Rooted, ELynx.Data.Tree |
| TreePos | ELynx.Data.Tree.Zipper, ELynx.Data.Tree |
| ultrametric | ELynx.Data.Tree.Measurable, ELynx.Data.Tree |
| unsafeGoPath | ELynx.Data.Tree.Zipper, ELynx.Data.Tree |
| values | ELynx.Simulate.PointProcess |
| zipTrees | |
| 1 (Function) | ELynx.Data.Tree.Rooted, ELynx.Data.Tree |
| 2 (Function) | ELynx.Data.Topology.Rooted |
| zipTreesWith | |
| 1 (Function) | ELynx.Data.Tree.Rooted, ELynx.Data.Tree |
| 2 (Function) | ELynx.Data.Topology.Rooted |