#' Longitudinal within-host Env single-genome amplification alignment.
#'
#' An alignment of 384 + 2 full-length HIV-1 envelope glycoprotein (env) gp160
#' amino-acid sequences sampled from 4 (w004) through 160 (w160) weeks
#' post-infection. The study participant identifier is 703010505, aka CH505.
#'
#' For the record, 397 sequences from CH505 are available in this sample
#' interval. Thirteen sequences have been excluded from this alignment,
#' two with unique long insertions relative to the TF (w009.33.KM284795 and
#' w136.B1.KC247403) and eleven with a shared 321-nt deletion, which most
#' likely results in an inviable Env. The two sequences with long insertions
#' explain why so many gapped columns in the alignment are unoccupied, i.e.
#' the gaps are place-holders for the long insertions. It is unclear whether
#' the shared deletions result from sequencing or replication error.
#'
#' @format
#' \describe{
#' \item{aas}{Sequence names contain up to three dot-separated fields,
#' indicating weeks post-infection, amplicon identifier, and database
#' accession number. Two additional sequences are the HXB2 reference for
#' numbering positions and the inferred transmitted-founder virus, which
#' matches multiple Envs. In the sequence text, asparagines in potential
#' N-linked glycosylation sites are indicated as "O". Gap characters ("-")
#' are inserted to maintain aligned sites. "Z" indicates a stop codon.
#' "X" indicates an incomplete or ambiguous codon.}
#' \item{tre}{The Newick-formatted phylogeny was inferred by phyml3 with HIVw
#' and Gamma4+I.}
#' \item{wpi}{The sample time-point at which the sequence was drawn, in weeks post-infection. Parsed from sequence names.}
#' }
#' @source \url{http://hiv.lanl.gov/components/sequence/HIV/search/d_search.com?spl_pub_id=16774}
#' @source \url{http://hiv.lanl.gov/components/sequence/HIV/search/d_search.com?spl_pub_id=18294}
#' @source \url{http://ncbi.nlm.nih.gov/pubmed/23552890}
#' @source \url{http://ncbi.nlm.nih.gov/pubmed/25065977}
"CH505"
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