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The recombination filter has been fixed for partition workflows. Recombination filtering can now be enabled via --recomb-filter as well as the original -x, --xtrafast flags. Fixes #157.
The --no-recruit has been fixed and replaced by --skip-ani-filter. Fixes #164.
"Recruitment" in general has been renamed to "Filtering" to be consistent with other methods.
Crashes gracefully when a partition's genomes are too divergent. Fixes #165.
Inputs with duplicate filenames no longer allowed, i.e. /path1/genome.fna and /path2/genome.fna cannot both be provided. This is because the .xmfa and .maf output files use the file stem as the "sample" name. Fixes #166.