Combine Repeat Libraries

Use the RepeatMasker tool queryRepeatDatabase.pl to extract taxon-specific repeats:

/exports/software/repeatmasker/repeatmasker-4-0-5/util/queryRepeatDatabase.pl \
       -species "taxon" > repeatmasker.taxon.fa

and combine with a repeatmodeller library. The output of queryRepeatDatabase.pl has an additional line at the begining before the start of the fasta format sequences so use tail -n+2 to skip the first line:

tail -n+2 repeatmasker.taxon.fa | cat - taxon.consensi.fa.classified > taxon.repeatlib.fa