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Exploring Phylogenetic Character Matrices: An In-Depth Analysis

This document provides a comprehensive overview of phylogenetic character matrices, highlighting their labels, descriptions, and structure. It details the organization of Operational Taxonomic Units (OTUs) and phylogenetic characters (PhyloChars), as well as their relationships within matrices. It includes unique identifiers for every element, alongside their associated properties and meta states, helping researchers efficiently navigate complex data sets. Essential for evolutionary biology studies, it offers insights into phylogenetic relationships and data management.

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Exploring Phylogenetic Character Matrices: An In-Depth Analysis

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  1. pPOD CDM

  2. Character Matrix Matrix label:String description:String otuSet:OTUSet otus:OTU [] otuIdx:Map<OTU,int> phyloChars:PhyloChar[] phyloCharIdx:Map<PhyloChar,int> rows:Row[] pPodVersion:long OTUSet label:String description:String matrices:Matrix[] otus:OTU[] pPodVersion:long PhyloChar label:String matrices:Matrix[] phyloCharStates :Map<int,PhyloCharState> properties :Map<String,String> pPodVersion:long 0..* * 0..* * OTU label:String matrices:Matrix[] otus:OTU[] pPodVersion:long * Row cells:Cell[] matrix:Matrix cells:List<Cell> cellIdx:Map<Cell,int> pPodVersion:long * PhyloCharState label:String state:long phyloChar:PhyloChar * * * Cell metaState:Enum{ASSIGNED,UNASSIGNED,INAPPLICABLE} uncertain:bool phyloCharStates:Set<PhyloChar> row:Row pPodVersion:long

  3. Tree Set TreeSet label:String description:String trees:Tree[] otus:OTU[] otuIdx:Map<int,Cell> otuSet:Set<OTU> OTUSet label:String description:String matrices:Matrix[] otus:OTU[] pPodVersion:long * 0..* * * * * OTU label:String matrices:Matrix[] otus:OTU[] pPodVersion:long Tree label:String newick:String treeSets:Set<TreeSet>

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