rdp-alignment:

rdp-alignment <subcommand> <options>

The Alignment tools package contains commands to do defined community analysis, pairwise alignment and hidden markov model (HMMER3 models, no training).

List of subcommands:

alignment-merger

- Merge alignments

pairwise-knn

- Compute k-nearest-neighbors by pairwise alignment

compare-error-type

- Detect insertion, deletion and substitution errors in sequences comparing to reference sequences

align-nucl-to-prot

- Transfer a sequence alignment from protein sequences to nucleotide sequences

rm-partialseq

- remove partial sequences based on pairwise alignment to reference sequences