SLiM-Tree is a simulation tool which automates pure population genetics simulations over phylogenetic timescales under realistic models of sequence-fitness relationships. For a full description of SLiM-Tree usage please refer to the user manual.
SLiMTree requires installation of Python3 and slim (https://messerlab.org/slim/). Required python packages are sys, argparse, BioPython, matplotlib, random, pandas, numpy, os, json, string and math. If using protein based fitness effects - java and c are also required.
To run SLiMTree run the command python3 SLiMTree -i <your input tree - in newick format>.
Additional arguments include:
-h: help - displays a help message showing options
-T: tool - specify whether you are using SLiM-Tree or SLiM-Tree-HPC (for parallelization)
-p: partition - the partition which scripts should be written to for SLiM-Tree-HPC
-t: time - the maximum amount of time that scripts should be run for before timing out on SLiM-Tree-HPC
-n: population size - the size of each population
-v: the mutation rate
-g: the length of the genome in codons
-r: recombination rate
-b: burn in multiplier - a value which will be multiplied by the population size to determine the length of the burn-in period to establish mutations
-k: sample size - the size of the sample of genomes to be output at the end of the simulation, users can specify number, 'all' for all genomes or 'consensus' for the consensus sequence
-sr: the ratio of the population that is split into each subpopulation in non-WF models of evolution
-G: the number of genes to be used in the genome - must be 1 if using protein based fitness effects
-C: the percentage of the genome which is coding - must be 1 if using protein based fitness effects
-hp: boolean specifying whether to model haploidy instead of diploidy
-c: boolean specifying whether supstitutions should be counted
-o: boolean specifying whether the generation of the simulation should be output (helps to keep track of longer simulations)
-B: boolean specifying whether simulations should be backed up
-w: boolean specifying whether a Wright-Fisher model should be used
-P: boolean specifying whether polymorphic states and percentages should be output
-s: boolean specifying whether the user provides a sequence
-f: link to fasta file for user provided sequences
-gb: link to genbank file for user profided fitnesses
-R: boolean specifying whether fitness profiles should be randomized, there must be an equal number of fitness profiles to the genome length if false
-fc: boolean specifying whether fitness effects should be calculated using site-heterogeneous fitness profiles. If false, fitness effects will be calculated using protein based structure and a pdb file must be provided
-pdb: link to pdb file containing structure to model
-pdbs: link to folder containing structurally diverse pdbs of approximately the same size as the supplied pdb to be used as a distribution of epistatic interactions
-cid: the chain id of the chain to be modelled in the main pdb
-cids: file containing the chain ids to be used in the distribution of epistatic interactions
-ct: the maximum distance that amino acids may be apart to be in contact with eachother
-jc: boolean specifying whether a Jukes-Cantor mutational matrix should be used. If false, users must specify a csv file containing mutational matrix.
-m: csv file containing mutational matrix defining the mutation rate from one nucleotide to another in alphabetical order (ie. A, C, G, T)
Users may also specify another file under -d with changes to parameters for different branches.
The folder DataPostProcessing contains scripts that were can be used for post processing of the output data and the folder.