Data from: Strong selection significantly increases epistatic interactions in the long-term evolution of a protein

Gupta A, Adami C

Date Published: April 15, 2016

DOI: http://dx.doi.org/10.5061/dryad.q66s5

 

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Title protease_sequences_1998_to_2006
Downloaded 10 times
Description HIV-1 protease sequences collected from HIV Stanford Database on 17th September 2013. The data spans 9 years (1998-2006) and sequences from treated (i.e. patients receiving one or more protease inhibitors) and untreated patients are in separate files.
Download protease_sequences_1998_to_2006.zip (665.5 Kb)
Download README (1.571 Kb)
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Title longitudinal_protease_sequences
Downloaded 3 times
Description HIV-1 protease sequences collected from HIV Stanford Database on 17 September 2013. The data represents HIV-1 protease sequences collected from same patients 'before' and 'after' a condition (i.e. 'treated' or 'untreated'). For example: sequences from patients who were initially untreated and then went on to receive treatment are titled "untreated_to_treated_protease_17SEP2013.src.blue.before.consensus_added" and "untreated_to_treated_protease_17SEP2013.src.blue.after.consensus_adde" respectively.
Download longitudinal_protease_sequences.zip (985.0 Kb)
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Title scripts
Downloaded 5 times
Description Python and matlab scripts to analyse protease sequence data
Download scripts.zip (2.984 Kb)
Download README (1.571 Kb)
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Title Figure_generator
Downloaded 5 times
Description iPython notebook to parse files and generate figures.
Download Figure_generator.ipynb (315.7 Kb)
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When using this data, please cite the original publication:

Gupta A, Adami C (2016) Strong selection significantly increases epistatic interactions in the long-term evolution of a protein. PLOS Genetics 12(3): e1005960. http://dx.doi.org/10.1371/journal.pgen.1005960

Additionally, please cite the Dryad data package:

Gupta A, Adami C (2016) Data from: Strong selection significantly increases epistatic interactions in the long-term evolution of a protein. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.q66s5
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