Since this question is tagged with R, you can use the DECIPHER package to perform sequence alignments and find the nearest neighbor (as requested in the comment by m.sabrysarhan). Assuming that you are starting with sequences in a FASTA file:
library(DECIPHER) # align the sequences seqs <- readDNAStringSet("<<REPLACE WITH PATH TO FASTA FILE>>") aligned <- AlignSeqs(seqs) # find the nearest neighbors d <- DistanceMatrix(aligned) diag(d) <- NA # prevent trivial distances of zero apply(d, 1, which.min) # indices of nearest neighbors
This returns a vector with the index of the nearest neighbor to each sequence. Hope that helps!
You can try ADOMA for nice figures for publication, it uses the clustal W algorithm but changes the output for easier interpretation.
The 16S rRNA molecule has secondary structure and an aligner that does not consider this is not good for phylogeny. If you want to find its closest relative just go to a specialized database such as the Ribosomal database project or the Silva database. There you will be able to find all related sequences from isolates and environmental sources and determine the novelty.