How to combine the outputs of repeat annotation softwares

How to combine the outputs of repeat annotation softwares

1

Hi,

I have been doing Repetitive sequence annotation on a new assembly genome. There is usually about four software for this purpose (e.g., TRF + RepeatProteinMasker + RepeatModeler&RepeatMasker ). Their applications confuse me a lot. Are they run independently? and then we combine the results generated by different software?
Or they are run one by one, the output masked fasta file from the former software is input file of the later software?

Thanks,


RepeatProteinMasker


TRF


RepeatMasker


RepeatModeler

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