A C program to calculate asymptotic maximum likelihood estimates (or pseudo-true parameter values) of parameters under the MSCI (multispecies coalescent [MSC] with introgression) model (a) of two species given that the true model is MSCM (MSC with migration; b-d), or vice versa, by minimizing the KL divergence. Assume one sequence per species, an infinite number of loci, and a Poisson model of mutations. Sequence length can be finite (n) or infinite.

Adapted from a program IMMSci2s written by Ziheng Yang for Jiao et al, 2020, using routines from PAML (paml.h and tools.c; Yang, 2007).

This program was used in Huang et al. (2022) and Thawornwattana et al (2024).

References:

• Huang et al. (2022) Inference of gene flow between species under misspecified models. Mol. Biol. Evol., 39(12):msac237

git clone https://github.com/ythaworn/iimmsci2s.git cd iimmsci2s make 

This should compile a program called iimmsci2. Example scripts are in script/.