Software/pipelines I have designed and coded for different research projects.
SelfingMutAccum
SelfingMutAccum simulates a self-fertilizing population who genomes contain a mixture of loci experiencing time constant selection (C-loci) and loci experiencing selection that fluctuates over time (L-loci). Selection fluctuations are auto-correlated in time and can change in strength and direction. Data is continually outputted at as the simulation runs.
Language: C++
simMutAccumTE
simMutAccumTE simulates a mutation accumulation (MA) experiment by inserting and/or deleting a number of transposable elements (TEs) in a diploid genome of a focal MA line while leaving the ancestral (ANC) genomes intact. After mutations are simulated in the given genome, paired-end reads are generated for all lines for downstream bioinformatic processing.
Language: Python
simMutAccumSV
simMutAccumSV simulates a mutation accumulation (MA) experiment by introducing structural variants (deletion, duplications, and inversions) into a diploid genome of a focal MA lines while leaving the ancestral genomes intact. After mutations are simulated in the given genome, paired-end reads are generated for all lines for downstream bioinformatic processing.
Language: Python