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Theoretical Estimates on the Expected Number of Mutations for Reconstructing Clonal Lineage Trees.

image

Installation

Instructions for Generating Perfect Binary Phylogeny.

Input

  • -n : number of leaves
  • -m : number of mutations
  • -t : random seed for tree generation
  • -s : random seed for mutation placement
  • -o : output_prefix

Outputs

  • output_prefix_tree.dot: dot format tree with mutations as edge labels
  • output_prefix_matrix.dot: mutation matrix of size (2n-1) * m, where n is number of leaves and m is number of mutations.

Instructions for Running

python src/generate_perfect.py -n 3 -m 10 -t 90 -s 90 -o "perfect"

This will create two files named perfect_tree.dot and perfect_matrix.dot.

Instructions for Generating K-Dollo Phylogeny from the Perfect Phylogeny.

Input

The first two arguments are for the perfect phylogeny cell (or clone) * mutation matrix and the perfect phylogeny in dot format. The remaining arguments are the following -

  • -k : K for K-Dollo loss.
  • --loss : loss probability
  • --mut-base : 0/1 (whether mutations are 0 or 1 indexed)
  • -A : K-dollo helper matrix file in tsv format (K-dollo completion of B)
  • -B : K-dollo mutation matrix file in tsv format (this is the input for reconstructing K-Dollo phylogenies)
  • --dot : K-Dollo output tree in dot format

Output

  • output.A: K-dollo helper matrix (K-dollo completion of B)
  • output.B: K-dollo mutation matrix (this is the input for reconstructing K-Dollo phylogenies)
  • output.dot: K-Dollo output tree in dot format

Instructions for Running

python src/generate_dollo_from_perfect.py perfect_matrix.tsv perfect_tree.dot -k 1 --loss 0.1 -s 90 --mut-base 0 -A onedollo.A -B onedollo.B --dot onedollo_tree.dot

Instructions for Generating Coalescent Trees.

We generate coalescent trees using CellCoal. The command for running the program we use is -

./cellcoal-1.2.0 -n10 \
    -s"num_leaves" \
    -l10000 \
    -e100000 \
    -g1.0e-05 \
    -j3000 \
    -k1 \
    -i1 \
    -b0 \
    -c0 \
    -C5 \
    -u1.0e-07 \
    -f0.3 0.2 0.2 0.3 \
    -r0.00 0.03 0.12 0.04 0.11 0.00 0.02 0.68 0.68 0.02 0.00 0.11 0.04 0.12 0.03 0.00 \
    -1 -2 -3 -4 -6 -v -x -W \
    -o"output_directory" \
    -#200011

Description of the parameters:

  • -n: number of replicates
  • -l : total sites in the genome
  • -e : population size
  • -g : exponential growth rate
  • -j : number of sampled site
  • -k : root branch length ratio
  • i : rate variation among branches
  • b : alphabet (0 for binary)
  • c : germline mutation rate
  • C : sequencing coverage
  • u : mutation rate per site per generation
  • f : base frequencies
  • r : mutation matrix ACGT x ACGT -1 -2 -3 -4 -6 -v -x -W \
  • o : output_directory \
  • #: random seed