simulate_recombination_families: Simulates the evolution of a family of sequences by taking...

In sams25/rcombinator_old: Tools to Simulate the Evolution of Genetic Sequences

Description

Simulates the evolution of a family of sequences by taking into consideration both point mutation and burst events This function does not return the sequences over time, but only the summary stats of the distances, and the pairwise distances at some timestamps

Usage

simulate_recombination_families(sequences, num_jumps, transition_matrix,
  burst_threshold, burst_mean, flip_probability, max_copy_number, dist_method,
  num_dist_matrices)

Arguments

sequences	The original sequences to begin with
num_jumps	The number of time steps to simulate for
transition_matrix	The transition matrix for the point mutations
burst_mean	The mean (for a Poisson distribution) increase in copy number during a burst event
burst_threshhold	The probability of a burst even occurring

Value

A list of sequences that have evolved over time with both point# mutation and recombination

sams25/rcombinator_old documentation built on May 28, 2019, 8:40 a.m.