User stories

Owned by Naim Matasci
Last updated: Jan 04, 2011Version comment
2 min read

User Personas

See here

Tools

Discrete ancestral character estimation

  • Anna has a phylogenetic tree in newick, nexus, nexml or phyloxml format
  • Anna has a table of multiple discrete trait data for the taxa present in the tree in cvs, nexus, tabulated or excel format.
  • For some traits, the data for some species are missing.

Phase 1

  • Anna wants to load the tree file in newick or nexus format
  • Anna wants to load the data table in csv or nexus format
  • Anna wants to combine the tree and the data
  • Anna wants to automatically match the taxa names in the table to the taxa names in the tree
  • Anna wants to be able to review and modify the matches
  • Anna wants to know the proportional likelihoods of the different states of a discrete trait at the internal nodes of the tree
  • Anna wants to be able to download the computed likelihoods
  • Anna needs a way to match the likelihoods to the internal nodes
  • Anna wants to visualize the likelihoods on her tree
  • Anna wants to estimate the rate of evolution of that trait and the associate measure of uncertainty
  • Anna wants to obtain a likelihood for her model
  • Anna wants to repeat the same analysis with a different starting parameter

Tests: https://pods.iplantcollaborative.org/wiki/display/iptol/DACE+Tests

Phase 2

  • Anna wants to load the data table in txt or excel format
  • Anna wants to select which characters to analyze
  • Anna wants to visualize the distribution of the traits on the taxa in the tree
  • Anna wants the tree and data matching to be more flexible
  • Anna wants to visualize larger trees, modify them and download them for presentations and publications.
  • Anna wants to be able to visualize more than one character at the time
  • Anna wants to add continuous data to her analysis
  • Anna wants to estimate multiple rates
  • Anna wants to define the evolutionary rate matrix

Continuous ancestral character estimation

  • Anna has a phylogenetic tree in newick, nexus, nexml or phyloxml format
  • Anna has a table of multiple continuous trait data for the taxa present in the tree in cvs, tabulated or excel format.
  • For some traits, the data for some species are missing.

Phase 1

  • Anna wants to load the tree file in newick or nexus format
  • Anna wants to load the data table in csv or nexus format
  • Anna wants to combine the tree and the data
  • Anna wants to automatically match the taxa names in the table to the taxa names in the tree
  • Anna wants to be able to review and modify the matches
  • Anna wants to estimate the trait values at the internal nodes of the tree and their associated uncertainties
  • Anna wants to be able to download the computed values
  • Anna needs a way to match the values to the internal nodes
  • Anna wants to visualize the values on her tree
  • Anna wants to obtain a likelihood for her model

Tests: https://pods.iplantcollaborative.org/wiki/display/iptol/CACE+Tests

Phase 2

  • Anna wants to load the data table in txt or excel format
  • Anna wants to select which characters to analyze
  • Anna wants to visualize the distribution of the traits on the taxa in the tree
  • Anna wants the tree and data matching to be more flexible
  • Anna wants to visualize larger trees, modify them and download them for presentations and publications.
  • Anna wants to be able to visualize more than one character at the time
  • Anna wants to add discrete data to her analysis

Geiger

deltaTree

fitContinuous

fitDiscrete

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