change the 99 to 1 less than the number of sequences you want: 

perl -e"BEGIN{$/=qq[\n>]}" -ple"$. == 99 && last;" yourfile.fasta >new
+file.fasta

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In reply to Re: How to write a perl script to grab the first 100 sequences to a 227,000 sequence file? by BrowserUk
in thread How to write a perl script to grab the first 100 sequences to a 227,000 sequence file? by radnorr

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