• Here, we present SLiM-Tree a flexible simulation tool which automates pure population genetics simulations over phylogenetic timescales under realistic models of sequence-fitness relationships. It is a simulation of across-species genome sequence datasets, including substitution histories and polymorphisms, without the standard suite of simplifying assumptions used in phylogenetics (e.g., mutation limited evolution/ weak mutation or infinite sites, limited mutation among competing allelic types between fixations, no polymorphism, etc.).
• How it works: It Employs SLiM (https://messerlab.org/slim/) to create a platform which can evolve populations with or without using Wright-Fisher model, allowing users to explore by relaxing simplified assumptions and models.
• Requirements: SLiMTree requires installation of Python3, R and SLiM. If using protein based fitness effects - java and c are also required.
•Required python packages: sys, argparse, BioPython, matplotlib, random, pandas, numpy, os, json, string and math.
•Required R packages: dplyr, BB, data.table, optparse, seqinr, doParallel, Rfast.• How to run SLiM_Tree: run the command python3 ../slim-tree/
For a full description of SLiM-Tree usage please refer to the user manual.
Additional arguments include:
-h: --help
show this help message and exit
-hpc: --high_performance_computing
boolean flag to turn on slim-tree high performance computing. Slurm is required
-fd AA_FITNESS_DISTRIBUTIONS: --aa_fitness_distributions AA_FITNESS_DISTRIBUTIONS
file containing a amino acid fitnesses
-p PARTITION: --partition PARTITION
partition to run Slurm on - required if using high performance computing
-t TIME: --time TIME
maximum time to run each simulation for - suggested time is the maximum time available for a partition -required if using high
performance computing.
-w: --nonWF
boolean flag to specify that a non-wright-fisher model should be used in lieu of a wright-fisher model.
-n POPULATION_SIZE: --population_size POPULATION_SIZE
starting population size for the simulation, default = 100
-b BURN_IN_MULTIPLIER: --burn_in_multiplier BURN_IN_MULTIPLIER
value to multiply population size by for burn in, default = 10
-r RECOMBINATION_RATE: --recombination_rate RECOMBINATION_RATE
recombination rate, default = 2.5e-8
-v MUTATION_RATE: --mutation_rate MUTATION_RATE
starting mutation rate for the simulation, default = 2.5e-6
-m MUTATION_MATRIX: --mutation_matrix MUTATION_MATRIX
CSV file specifying a mutation rate matrix, matrix should be either 4 by 4 or 4 by 64 specifying rates from nucleotide
to nucleotide and tri-nucleotide to nucleotide respectfully. Nucleotides and tri-nucleotides should be in alphabetical
order with no headers. If mutation rate matrix is supplied, mutation rate will be ignored
-d TREE_DATA_FILE: --tree_data_file TREE_DATA_FILE
file to change the population size for specific branches using YAML formatting. When using HPC, other parameters may
also be changed.
-g GENOME_LENGTH: --genome_length GENOME_LENGTH
length of the genome - amino acids, default = 300
-G GENE_COUNT: --gene_count GENE_COUNT
number of genes to be simulated by the model, default = 1
-C CODING_RATIO: --coding_ratio CODING_RATIO
ratio of the genome which is coding, default = 1.0
-f FASTA_FILE: --fasta_file FASTA_FILE
fasta file containing ancestral sequence (amino acids), replaces random creation of ancestral sequence. Fitness
profiles for each amino acid are required
-k SAMPLE_SIZE: --sample_size SAMPLE_SIZE
size of sample obtained from each population at a tree tip at the end of the simulations.Input 'all' for the every
member of the tree tip samples and consensus for the consensus sequence of the population at each tip. default = all
-sr SPLIT_RATIO: --split_ratio SPLIT_RATIO
proportion of a population that goes into the first daughter branch at a tree branching point in non-wright fisher
models. must be ratio between 0 and 1.0. default = 0.5
-c: --count_subs
boolean flag to turn on substitution counting. This will slow down simulations
-o: --output_gens
boolean flag to output every 100th generation. This can be helpful in tracking simulation progression
-B: --backup
boolean flag to turn on backups of the simulations, allowing a restart of simulations if required. This will increase space and
time complexity
-P: --polymorphisms
boolean flag to turn on the creation of file specifying all polymorphic and fixed states at the end of a branch
-S: --calculate_selection
boolean flag that turns on calculations of selection by counting synonymous and non-synonymous fixed substitutions• Usage: slim-tree [-h] [-fd AA_FITNESS_DISTRIBUTIONS] [-hpc] [-p PARTITION] [-t TIME] [-w] [-n POPULATION_SIZE] [-b BURN_IN_MULTIPLIER] [-r RECOMBINATION_RATE] [-v MUTATION_RATE] [-m MUTATION_MATRIX] [-d TREE_DATA_FILE] [-g GENOME_LENGTH] [-G GENE_COUNT] [-C CODING_RATIO] [-f FASTA_FILE] [-k SAMPLE_SIZE] [-sr SPLIT_RATIO] [-c] [-o] [-B] [-P] [-S] input_tree codon_stationary_distributions
The folder DataPostProcessing contains scripts that can be used for post processing of the output data and the folder.