Example1:
perl -e 'while(<>) {if($_=~/^>/) {print $_;} else {$_=~tr/ATCG/TAGC/; 
+print $_;}}'  FILE
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Use -n to replace the while loop:

perl -nle 'if($_=~/^>/) {print $_;} else {$_=~tr/ATCG/TAGC/; print $_;
+}' FILE
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Do away with the unnecessary explicit references to $_:

perl -nle 'if(/^>/) {print;} else { tr/ATCG/TAGC/; print; }' FILE
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Recognise that every line is being printed, so -p can replace the explicit print statements:

perl -ple 'if(/^>/) { ; } else { tr/ATCG/TAGC/; }' FILE
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Rearrange to do away with the empty if body:

perl -ple 'tr/ATCG/TAGC/ unless( /^>/ );' FILE
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UPDATE: a final step:

perl -ple '/^>/ or tr/ATCG/TAGC/' FILE
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