/dupcoal

Simulate gene trees under a model that allows copy number hemiplasy.

Primary LanguagePython

dupcoal

Simulate gene trees under a model that allows copy number hemiplasy.

For an extended description of the simulator, please see 'Extended_Description_v1a.pdf'.

Arguments

  • stree

    • type = str
    • help = Path to file with newick formatted species tree to use for simulation. Branch lengths should be in coalescent units.

  • mu_par

    • type = float
    • help = loss rate.

  • lambda_par

    • type = float
    • help = duplication rate.

  • reps

    • type = int
    • help = Number of gene families to simulate.

  • output

    • type = str
    • help = Folder for storing results.

Outputs

  • rep_i.tre = final simulated gene family tree for replicate i.
  • rep_i_alltrees_mutated.tre = all full subtrees (after the placement of mutations) for replicate i. Note that when trees only have a single branch, they do not show up appropriately in FigTree.
  • rep_i_alltrees_unmutated.tre = all full subtrees (prior to the placement of mutations) for replicate i.
  • rep_i.log = A log file indicating the total numbers of duplications and losses for the replicate. Also indicates when all copies were lost, and has counters for different types of deep coalescence events.
  • rep_i.tsv = A table indicating for each branch in the species tree, which subtrees were concordant.
  • rep_sptree_i.tre = An annotated species tree for matching branches to those in the tsv file.

Log file explanation

  • Total duplications: number of duplications
  • Total losses: number of losses
  • Copy Number Hemiplasy (CNH): number of cases in which a mutation is placed on a branch that does not exist in the branch of the species tree on which the mutation occurred.
  • Rasmussen and Kellis CNH: number of cases in which a mutation is placed on a branch that does exist in the species tree, but does not match the current branch of the species tree. This is the phenomenon described as hemiplasy in Rasmussen and Kellis (2012, Figure 2B)
  • All NNI: This includes the number of discordant branches in the parent and daughter trees and the number of NNIs that should be needed to reconcile discordance that occurs when coalescing subtrees.
  • All ILS (DLCPar): This includes the number of parent or daughter trees that are discordant and the number of times that a subtree joined a branch that did not match it in terms of taxon composition.

Example Usage

python3 dupcoal_v2.0.0.py --stree sp_tree.tre --mu_par 0 --lambda_par 0.3 --reps 10 --output example