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There's no point in using g if you're anchoring the regex to the beginning of the line.
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terdon ♦
terdon ♦
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Or a bit more verbose ...

perl -nle 'push @res, $_  while s/^>//g;; END {print  join "\n",@res}' myfile.fa

Or a bit more verbose ...

perl -nle 'push @res, $_  while s/^>//g; END {print  join "\n",@res}' myfile.fa

Or a bit more verbose ...

perl -nle 'push @res, $_  while s/^>//; END {print  join "\n",@res}' myfile.fa
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M__ ♦
M__ ♦
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Or a bit more verbose ...

perl -nle 'push @res, $_  while s/^>//g; END {print  join "\n",@res}' myfile.fa