All scripts have hard-coded input and output destinations. If you want to run them for yourself, you will need to adjust these destinations in each script as you go.
This script simulates birth-death trees under the constant rate birth-death process with incomplete sampling. The speciation rate, extinction rate, and sampling fraction are sampled from a unifrom distribution (0,1). However, we force the extinction rate to be smaller than the speciation rate.
This script will run iqtree on all alignment files to find the best-fit GTR models, base frequencies, and branch lengths for each dataset. (note there is a threads argument at the top of the script which you should change as appropriate, it also relies on GNU parallel)
This script will create a table with the GTR parameters, base frequencies and proportion of invariant sites from all partitions as have been estimated by IQ-TREE. the output file will be saved in the root directory as GTRparam.csv
This script will create a table with the branch lengths from all datasets as have been estimated by IQ-TREE. the output file will be saved in the root directory as BranchLen.csv
This script will generate non-SRH GTR matrices that use to simulate alignments under non-SRH conditions with inheritance scheme. The idea is that each branch will have its own substitution model or/and base frequencies that are derived from the initial parameters (substitution model or/and base frequencies). The contribution of the initial parameters depends on the inheritance weight of the simulation - inheritance weight of 0 means no contribution at all, and all the matrices along the tree are independent. inheritance weight of 1 means all the matrices along the tree are identical and equal to the initial matrix. In order to run this script you need the software Hetero2 that is available on Github. In addition to the non-SRH parameters, this script will assign new branch lengths from the empirical distribution to the trees that were simulated under the birth-death process > run birth-death.R. The simulated alignments will be saved in the root directory.
In addition to simulations under inheritance scheme, this script will generate non-SRH GTR matrices that use to simulate alignments under non-SRH conditions. However, under this scheme there are only two matrices along the tree - the initial matrix (Q0) and another matrix (Q1). the script will randlomy choose two subtrees that are not descendants or sisters for each other and assign matrix Q1 to all the branches in these two subtrees. In order to run this script you need the software Hetero2 that is available on Github. In addition to the non-SRH parameters, this script will assign new branch lengths from the empirical distribution to the trees that were simulated under the birth-death process > run birth-death.R. The simulated alignments will be saved in the root directory.