The impact of sequencing and genotyping errors on Bayesian analysis of genomic data under the multispecies coalescent model

BPP control files used in "The impact of sequencing and genotyping errors on Bayesian analysis of genomic data under the multispecies coalescent model" by Jiayi Ji, Paschalia Kapli, Tomas Flouri, and Ziheng Yang. This repository involves control files for BPP used for simulating data and running analysis of Species tree inference (A01) Parameter estimation under the MSC-I model (A00.I) Parameter estimation under the MSC-M model (A00.M) For each setting, there are: A simulation control file for generating datasets under the MSC/MSC-I/MSC-M model with sequencing errors at a specified rate. Two analysis control files for running BPP on the simulated dataset — one with phasing and one without phasing. For instance, in the path A01/5X_0.01/treeB_0.0025/L40_N250_S1: sim.A01.ctl: Simulates sequence alignments under treeB with θ = 0.0025 (fig. 3). Data are simulated at depth of 5X with a base-calling error rate of 0.01, which contains 40 loci, one sequence per species, and 250 sites per sequence. A01.bpp.ctl: Used for standard species tree inference in BPP, enabling analytical phasing of diploid sequences. A01.bpp-ambiguity.ctl: Used for BPP runs without phasing, treating heterozygotes as ambiguities.