Add filter and orient with HMMs

[iimog]

Currently only dispr is included for filtering and orientation. However HMMs would make sense as well. Especially, as we have good HMMs for the borders of the ITS2.

[iimog]

Possible problem. We want to search DNA so in HMMER >=3.1 there are special tools for that nhmmer and nhmmscan. Those have the following purpose (see manual):

• nhmmer Search a DNA sequence, alignment, or profile HMM against a DNA sequence database. (BLASTN-like)
• nhmmscan Search a DNA sequence against a DNA profile HMM database.

But what we would need is the DNA equivalent to:

• hmmsearch Search a protein profile HMM against a protein sequence database.

However this does not exist. First experiments indicate that both nhmmer and nhmmscan could work for our purpose but there might be problems with either large sequence databases or long query sequences.

[iimog]

Important: hmmsearch only searches the forward strand (as it would with proteins). nhmmer also considers the reverse strand. So either switch over to that or run hmmsearch on both the normal sequences and the rc of all sequences.