while (<MYFILE>) #this is my opened file
{
  {                   
    next if /^\s*File/; #remove line starting with filename

    my ($id, $seq) = split; # The my is important  
    push @{$species{$id}}, $seq;        
  }        
}

# later...

while ( ($key, $sequence) = each %species ) {
  print $key, "\t", join ":", @$sequence;
}

# Which will out your key, followed by a tab, 
# followed by all your sequences (however many 
# there are) separated by colons