---
name: "rdp-alignment"
section: "1"
platform: "linux"
package: "rdp-alignment"
version: "1.2.0-8"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/rdp-alignment"
---

# rdp-alignment(1)

Ribosomal Database Project (RDP) alignment tools package

## NAME

rdp-alignment: - Ribosomal Database Project (RDP) alignment tools package

## SYNOPSIS

**rdp-alignment** *\<subcommand\> \<options\>*

## DESCRIPTION

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

## OPTIONS

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