Modifications of scripts from https://github.com/mossmatters/phyloscripts/tree/master/alleles_workflow and phyloscripts in general (notably haplonerate.py) to make them work (for me at least); plus SLURM submission scripts with various bash commands to help the process.
Various dependencies: see the readme at above link.
Please cite Kates, H.R., Johnson, M.G., Gardner, E.M., Zerega, N.J.C. & Wickett, N.J. 2018. Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus. American Journal of Botany. 105(3):404–416. DOI: 10.1002/ajb2.1068.