Quick, de-interleave it!
There are one-liners that never get old. This is one of them.
$ perl -MBio::SeqIO -e
'my $seqin = Bio::SeqIO->
new(-fh => \*STDIN, -format => 'fasta');
while (my $seq = $seqin-> next_seq)
{ print ">", $seq-> id, "\n", $seq-> seq, "\n"; }'
< interleaved.fasta > deinterleaved.fasta
Update 28-Jan-2019:
Over time, I came to find working with BioPerl uncomfortable, as its clean installation is just not well-supported on Linux. Thus, I have found myself relying on this method more and more, assuming that the line breaks of the input file are LF (and not CRLF):
$ INF=interleaved.fasta
awk '/^>/ {printf("\n%s\n",$0);next; } \
{ printf("%s",$0);} END {printf("\n");}' \
< $INF | tail -n +2 \
> ${INF%.fasta*}_deint.fasta
Die