Patient p1

# samples
Time [days] RNA templates F1 F2 F3 F4 F5 F6
122 33 ok ok ok ok ok ok
562 460 ok ok ok ok low ok
1084 380 ok ok ok ok low ok
1254 730 ok ok ok ok low ok
1282 730 ok ok ok ok low ok
1393 440 ok ok ok ok low ok
1861 650 ok ok ok ok low ok
2303 2 000 ok ok ok ok low ok
2578 19 000 ok ok ok ok low ok
2639 16 000 ok ok ok ok low ok
2922 33 000 ok ok ok ok ok ok
2966 43 000 ok ok ok ok ok ok

Phylogenetic tree of V3 in patient p1.

  • RNA template counts are estimated two limiting dilutions series using fragment 4
  • An orange label for a fragment indicates problematic amplification and possible loss of variation.
  • A red label indicates a missing fragment.
Link color:
  • To display a phylogenetic tree of a particular region of the genome, select it in the pull-down menu.
  • Choices ending on minor include minor haplotypes from each time point, others display only consensus sequences
  • The size of the Tip circles indicate the frequency of the corresponding haplotype.
  • HIV recombines. Hence there trees don't necessarily depict the actual evolutionary history of the chosen part of the genome.
  • These are approximate maximum-likelihood trees generated with Fasttree

Note: low diversity might be due, in addition to biological reasons, to a low RT-PCR efficiency in a specific amplicon.

  • The top panels show divergence and diversity averaged in sliding windows of ??? bases for every position of the genome at particular time point.
  • The time point can be varied by moving the slider at the bottom.
  • The graph shows coverage at every postition in the genome.
  • The red line indicates the number of amplified RNA templates estimated from two limiting dilution series.
  • The each fragment corresponds to one of the peaks in coverage. Coverage tends to be lower towards the end of the fragments.
  • Where fragments overlap, the sum of reads from both fragments is reported
  • Some fragments amplify less well than other (F5 in particular). These tend to have low coverage or are sometimes missing completely.
  • The top panel shows single nucleotide polymorphism (SNP) frequencies through time. Color indicates position along the genome.
  • The panel below shows SNP frequencies at each position for a given time point. The color of each point equals that of the corresponding trajectory in the top panel.
  • The time point shown in the second panel can be chosen via the slider on top.
  • Clicking on an annotated element of the genome will zoom into that element.
Annotated genome sequence in genbank format:

Precompiled alignments

These alignments are premade for regions of general interest.

New alignments

Generate alignments for a custom genomic region.

From/To require HXB2 coordinates (both ends included).

NOTE: A few minutes might elapse while we prepare your data.

PBMC samples available for patient p1
Sample years on treatment good reads hypermutated
DNA 1 7.9 reads reads
DNA 2 9.9 reads reads
DNA 3 10.3 reads reads
  • Times indicate sampling times relative to start of treatment.
  • "Good" reads are those that map to p17gag and did not have obvious signs of hypermutation.
  • Hypermutated reads are those that map to p17gag and showed an excess of G-to-A mutations.

Tree of p17 before (RNA) and on treatment (DNA).