hiv.ref: Population-level (between-host) HIV-1 Subtype reference...
In phraber/pixelgram: Pixel View with Accompanying Phylogram of Sequence Alignment

An alignment of 39 M HIV-1 nucleotide sequences selected to represent the non-recombinant M group clades A through K.

hiv.ref

nts: Sequence names contain five dot-separated fields, to indicate clade, country sampled, year sampled, common name, and database accession number. The sequence Ref-H.B.00.00B4001.FJ711703 contains IUPAC ambiguity codes.
tre: The Newick-formatted phylogeny was inferred by phyml3 with GTR and Gamma4+I.
clade: M-group subtype (clade) designation, parsed from the sequence name.

Genome-length aligned sequences are available at the link listed below. Data here include only the gp41 ectodomain, a 399-nt region (HXB2 sites 7881 through 8279) excised from the envelope glycoprotein (env), i.e. gp160 nucleotides 1657-2055 (gp160 amino acids 553-685) and gp41 nucleotides 124-522 (gp41 amino acids 42-174).

http://hiv.lanl.gov/content/sequence/HIV/REVIEWS/RefSeqs2005/Refseqs05.html

http://hiv.lanl.gov/content/sequence/NEWALIGN/Align.html

phraber/pixelgram documentation built on May 25, 2019, 6:02 a.m.