Calculate a distance matrix
To calculate a distance matrix of a group of sequences, you need to:
1. Make an alignment, using INFERNAL for 16S rRNA gene of archaea and bacteria, and 28S rRNA gene of fungi; or using HMMER3.1b1 to align protein sequences. Both alignment tools align sequences to pre-built, gene-specific alignment models, which can be found in RDP.
2. Remove unalignable positions using RDP ReadSeq tool (command: 'java -jar /mnt/research/rdp/public/RDPTools/ReadSeq.jar to-fasta -m "#=GC RF")
3. Calculate the distance matrix using RDP Clustering tool with the alignment file made in step 2.