Align sequences

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1. Use INFERNAL to align sequences to archaeal 16S rRNA model , bacteria 16S rRNA model, or to fungal 28S rRNA model pre-built by RDP.

2. Use HMM3.1b2 to align protein sequences to protein family specific HMMs prebuilt by RDP.

3. Align nucleotide coding sequences to their protein alignment using RDP AlignmentTools.

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