Datasets

The following datasets were analyzed in GenGIS: A geospatial information system for genomic data (Parks et al., Genome Res., 2009):

• GOS dataset: taxonomic diversity of Atlanatic seaboard sites from the Global Ocean Sampling expedition.

• HIV-1 dataset: geographic distribution of non-recombinant HIV-1 subtypes in Africa

• ISEA mtDNA dataset: phylogenetic distribution of mtDNA haplogroup E, using hypervariable segment I (HVS-I) sequences from Southeast Asia.

The following datasets were analyzed in Tracking the evolution and geographic spread of Influenza A (Parks et al., PLoS Currents: Influenza, submitted Aug. 25, 2009):

• Location file containing the latitude and longitude of each geographic location, each of which could contain one or more isolates.
• Sequence file with one row per isolate, containing metadata information including collection date and polymorphic amino acid sites.
• Phylogenetic tree of 203 complete S-OIV sequences as determined by RAxML.
• Polymorphic subtree of 136 complete S-OIV sequences containing polymorphisms at neuraminidase sites 106 and 248.
• Panmixia subtree of 16 complete S-OIV sequences demonstrating the rapid, global spread of S-OIV.
• Stream video showing the temporal and geographic spread of neuraminidase site N248D.
  • Python script used to create the above video (requires the location and sequence files above along with a world map).
• Stream video showing the geophylogeny of a subtree exhibiting polymorphism at neuraminidase site 248.
  • Python script used to create the above video (requires the location and sequence files along with one of the phylogenetic trees given above plus the world map).