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I often find myself using AliTV in quick mode (providing a list of fasta files to alitv.pl instead of a .yml file) just to let AliTV create the proper .yml file. Then cancel, adjust the .yml and run alitv.pl again with this modified .yml. While this works just fine it is a bit of a hack and might be worth considering as a feautre. The idea is a --create_yml or --yml_only parameter that if present stops AliTV after creating the .yml file.
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