This is a data and script file repository for SCUEAL - an algorithm to subtype and determine the mosaic structure of HIV-1 strains.
Downloadable items
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The manuscript describing the method and its performance on real and simulated data is available from PLoS Computational Biology -
HyPhy batch files, reference alignments and other files implementing the method can be downloaded [from GitHub]. Installation and usage instructions can be found in the README.pdf file.
Please see the manuscript for the explanation on the next items.
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A FASTA file and SCUEAL screening results for the surveillance sample described by Salemi et al: a summary comma separated file; see the README.pdf file for an explanation of fields and individual postscript plots. [Bulgaria.zip]
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Data for parametric simulations in Table 1 of the manuscript can be downloaded from http://darwin.uvigo.es/temporal/gasp2.html
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A FASTA file and screening results (summary only) for the shuffling simulation using HIV-1 pol sequences (see the manuscript for details) [Shuffled.zip]
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A directory (stratified by annotated subtype) of SCUEAL analyses of every RT sequence from the Stanford Drug Resistance database. [Stanford.tar.bz2] Warning: this archive is approximately 450MB in size and it expands to about 24000 files containing over 4GB of data.
