The sintax command has been improved in several ways in this version of vsearch. Please note that several details of this algorithm is not clearly described in the preprint, and the implementation in vsearch differs from that in usearch.
The former vsearch version did not always choose the most common taxonomic entity over the 100 bootstraps among the database sequences with the highest amount of word similarity to the query. Instead, if several sequences had an equal similarity with the query, the sequence encountered in the earliest bootstrap was chosen. The confidence level was calculated based on this sequence compared to the selected sequences from the other 99 bootstraps. This could lead to a suboptimal choice with a low confidence. In the new version, the most common of the sequences with the highest amount of word similarity across the 100 bootstraps will be selected, and ties will be broken randomly.
Another problem with the old implementation was that if several sequences had the same amount of word similarity, the shortest one in the reference database would be chosen, and if they were equally long, the earliest in the database file would be chosen. A new option called sintax_random has now been introduced. This option will randomly select one of the sequences with the highest number of shared words with the query, without considering their length or position. This avoids a bias towards shorter reference sequences. This option is strongly recommended and will probably soon be the default.
Furthermore, a ninth taxonomic rank, strain (letter t), is now recognized. The speed of the sintax command has also been significantly improved at least in some cases. Run vsearch with the randseed option and 1 thread to ensure reproducibility of the random choices in the algorithm.