Actually, I tried Galaxy to cut my overrepresent sequence, but my sequence is on 5' of read and reported as Illumina Single End PCR Primer 1. So I used Galaxy fastx-clipped but it can only clip adapt or primer sequence in 3'. So I changed to use cutadapt tool and cut 5' of read, it works well. However, I got a wide variety of length of reads after that from 0 bp to 88 bp
If you're aligning your reads for phylogenetic analysis you'll have to have a matrix that is all the same length, so in that case, you'll have to trim. As Ido Tamir recommended, the FASTX TRIMMER from the Hannon Lab is very good.