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

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