Reconstructing the viral histories of human, simian, and prosimian immunodeficiency viruses across multiple evolutionary timescales
Data and analysis files for the manuscript: “Reconstructing the viral histories of human, simian, and prosimian immunodeficiency viruses across multiple evolutionary timescales” This repository contains the sequence alignments, BEAST XML files, phylogene
Data and analysis files for the manuscript:
“Reconstructing the viral histories of human, simian, and prosimian immunodeficiency viruses across multiple evolutionary timescales”
This repository contains the sequence alignments, BEAST XML files, phylogenetic tree outputs, and R code used to reconstruct the evolutionary history of HIV, SIV, and pSIV lineages using the Prisoner of War (PoW) framework.
Fullgenome.fasta
Full-genome alignment of the complete lentivirus dataset used in the study, including HIV, SIV, and pSIVgml.hiv_clock_dataset.fasta
Time-stamped HIV-1 group M alignment used to estimate short-term substitution rates for each non-recombinant region (NRR).
For each non-recombinant region (NRR), the repository contains two BEAST XML files:
NRR_*.xml
BEAST XML files used to infer the ultrametric genetic-distance trees for each NRR under the HKY substitution model. These trees provide the input distance trees for the downstream PoW transformation
These XML files correspond to the analyses used to generate the posterior tree files from which the PoW-transformed time-scaled divergence trees were constructed.
NRR_*_dated_iso_v1.xml
Isochronous analysis for the relevant NRR.NRR_*_dated_hetero_v1.xml
Heterochronous (tip-dated) analysis for the relevant NRR.
These two sets of XML files were used for Bayesian Evaluation of Temporal Signal (BETS) via stepping-stone sampling to compare isochronous and heterochronous models and assess temporal signal in each NRR.
* denotes the NRR number.
MCC_filtered_PoWtransformed_NRR_*.tree
Maximum clade credibility (MCC) trees obtained after applying the PoW distance-to-time transformation to the NRRs with sufficient temporal sign📤 Share this page
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Files are hosted on the source repository. Click download to access the full dataset.