If you're interested in calculating population-genetic statistics in sliding windows from .ms files using python, here are some scripts that you can use.

Here are scripts that use either a single or multiple .ms files and summarize a number of allel frequency and LD-based statistics:

https://github.com/paruljohri/Scripts_PopGen_Statistics_Python/blob/main/statistics_slidingwindow_pylibseq_general_1rep.py

https://github.com/paruljohri/Scripts_PopGen_Statistics_Python/blob/main/statistics_slidingwindow_pylibseq_general_reps.py

Here is a script that will summarize FST-based statistics and also allele frequency-based statistics for each individual population for the same sliding windows:

https://github.com/paruljohri/Scripts_PopGen_Statistics_Python/blob/main/statistics_slidingwindow_pylibseq_general_reps_fst.py

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