HIV Phylogenetic Placement Service

Purpose: To help decide whether a sequence belongs to a known or new clade, this service reports phylogenetic relatedness of a query sequence with reference sequences in known clades. The query sequence is automatically aligned with reference sequences before analysis.

Instructions:

1. Enter a FASTA-formatted sequence. (Copy and paste your sequence into the text box.)

2. Choose between analysis methods:

• Pairwise Distances summarizes the distribution of uncorrected pairwise distances for query and reference sequences. An "Analysis Depth" menu appears when you choose this option, which allows you to specify the distances to be reported.

• Branching Index computes a profile of phylogenetic relatedness with known subtypes from overlapping windows over the length of your sequence.

3. Click on the "Submit" button to start the analysis.

Please consult the documentation for methodological details.