Analyses
Viral load and CD4+ counts Viral load and CD4+ counts Genome sequences Genome sequences Consensus sequences Consensus sequences Phylogenetic trees Phylogenetic trees Divergence and diversity Divergence and diversity Local divergence and diversity Local divergence and diversity Coverage Coverage Single nucleotide polymorphisms Single nucleotide polymorphisms Haplotypes Haplotypes

Haplotypes

Local haplotypes are used to study the joint evolution of sites within a genomic region, such as proteins or RNA structures.
They contain linkage information on neighbouring sites within approximately 400 bp. They are derived directly from the reads without any post-processing beyond trimming.
Keep in mind that although we tried to minimize the number of PCR cycles, some in vitro recombination is expected.

Choose one option:

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.