text: user48: After some unexpected results (and previously reported) I heard that there are other tools for finding similar sequences besides blast that are faster and more accurate.
  I only found hmmer, but I don't know if it is faster and more accurate.
  Is there any review comparing such tools? A quick google scholar search didn't report anything useful.
  I want to search with short DNA sequences (~400), mainly interested for taxonomic imputation so I'll be looking for similar sequences and not distant homologs. I won't try to model genes and the sequence will be unspliced as it is from direct sequencing of a a region of the 16S gene.
  
  user1802: Besides generic nucleotide aligners, there are also more specialized tools for the alignment of 16S amplicon sequences, e.g. SINA (article, software) which is part of SILVA
  
  user3748: As I understand, the software tool Lambda is a viable, yet lesser known alternative to BLAST in the context of taxonomic classification of NGS data.
  
original_text: 48: <p>After some <a href="https://bioinformatics.stackexchange.com/questions/2846/why-does-a-very-strong-blast-hit-get-lost-when-i-change-num-alignments-num-desc">unexpected results</a> (and <a href="https://blastedbio.blogspot.com/2018/11/blast-max-alignment-limits-part-four.html" rel="nofollow noreferrer">previously reported</a>) I heard that there are other tools for finding similar sequences besides blast that are faster and more accurate.</p>
  
  <p>I only found <a href="http://hmmer.org/" rel="nofollow noreferrer">hmmer</a>, but I don't know if it is faster and more accurate.</p>
  
  <p>Is there any review comparing such tools? A quick google scholar search didn't report anything useful.</p>
  
  <p>I want to search with short DNA sequences (~400), mainly interested for taxonomic imputation so I'll be looking for similar sequences and not distant homologs. I won't try to model genes and the sequence will be unspliced as it is from direct sequencing of a a region of the 16S gene.</p>
   1802: <p>Besides generic nucleotide aligners, there are also more specialized tools for the alignment of 16S amplicon sequences, e.g. SINA (<a href="https://academic.oup.com/bioinformatics/article/28/14/1823/218226" rel="nofollow noreferrer" title="SINA article">article</a>, <a href="https://github.com/epruesse/SINA" rel="nofollow noreferrer" title="SINA at github">software</a>) which is part of <a href="https://www.arb-silva.de/" rel="nofollow noreferrer" title="SILVA website">SILVA</a></p>
   3748: <p>As I understand, the software tool <a href="https://academic.oup.com/bioinformatics/article/30/17/i349/199474" rel="nofollow noreferrer">Lambda</a> is a viable, yet lesser known alternative to BLAST in the context of taxonomic classification of NGS data.</p>
  