* The PhenoSeq "unknown" subtype option is temporarily out of order. It will be up and running again soon. In the meantime, please use an alternative HIV subtyping tool (such as COMET; http://comet.retrovirology.lu/ or REGA; http://www.bioafrica.net/rega-genotype/html/) then select the appropriate PhenoSeq algorithm.

Please submit unaligned sequence(s) containing the V3 region only in FASTA format with a unique name for each sequence, e.g.
>seq_1
CTRPNNNTRKSIRIGPGRAFVTIGKIGNMRQAHC

The PhenoSeq platform will align submitted sequence(s) to HXB2 using the
European Bioinformatics Institute Multiple Sequence Alignment tools website
(Larkin, M. A et al., Bioinformatics (Oxford, England) 23 (21):2947-8).

You may submit a FASTA file or text with any number of sequences. If a submission contains more than 499 query sequences, the tool will process them in batches of up to 499 queries, preserving the order in the FASTA. For each batch, the HXB2 reference must be included as the first entry, a multiple sequence alignment is performed, and tropism predictions are generated for the queries in that batch.
Example: a submission with 502 sequences will be processed as one batch of 499 queries + HXB2, followed by a second batch of 3 queries + HXB2.
There is no limit on the total number of sequences per submission, but each alignment batch is capped at 499 queries. If you need sequences from the same donor to be aligned together, please submit each donor’s sequences as separate submissions.