Difference between revisions of "Datasets"
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| − | The following datasets were analyzed in ''Tracking the evolution and geographic spread of Influenza A'' (Parks et al., PLoS Currents: Influenza | + | The following datasets were analyzed in ''Tracking the evolution and geographic spread of Influenza A'' ([http://knol.google.com/k/donovan-parks/tracking-the-evolution-and-geographic/1049pdwpgoubk/1?collectionId=28qm4w0q65e4w.1&position=2#| Parks et al., PLoS Currents: Influenza: RR1014]): |
*[[Media:h1n1locations.zip|Location file]] containing the latitude and longitude of each geographic location, each of which could contain one or more isolates. | *[[Media:h1n1locations.zip|Location file]] containing the latitude and longitude of each geographic location, each of which could contain one or more isolates. | ||
*[[Media:aa_sequences.zip|Sequence file]] with one row per isolate, containing metadata information including collection date and polymorphic amino acid sites. | *[[Media:aa_sequences.zip|Sequence file]] with one row per isolate, containing metadata information including collection date and polymorphic amino acid sites. | ||
*[[Media:H1N1_Concatenate_Midpoint.zip|Phylogenetic tree]] of 203 complete S-OIV sequences as determined by RAxML. | *[[Media:H1N1_Concatenate_Midpoint.zip|Phylogenetic tree]] of 203 complete S-OIV sequences as determined by RAxML. | ||
| − | *[[Media: | + | *[[Media:H1N1_NA248_ND_Subtree.zip|Polymorphic subtree]] of 136 complete S-OIV sequences containing polymorphisms at neuraminidase sites 106 and 248. |
| − | *[[Media:H1N1_Panmixia_Subtree.zip| | + | *[[Media:H1N1_Panmixia_Subtree.zip|Dispersal subtree]] of 16 complete S-OIV sequences demonstrating the rapid, global spread of S-OIV. |
| + | *[[Media:Aneides.zip|Aneides Dataset]] containing sample files of Aneides Lugubris on the West Coast of the USA. | ||
*[[Media:GenGIS_NA248_Polymorphism.swf|Stream]] video showing the temporal and geographic spread of neuraminidase site N248D. | *[[Media:GenGIS_NA248_Polymorphism.swf|Stream]] video showing the temporal and geographic spread of neuraminidase site N248D. | ||
| − | + | *[[Media:GenGIS_NA248_ND_Geophylogeny.swf|Stream]] video showing the geophylogeny of a subtree exhibiting polymorphism at neuraminidase site 248. | |
| − | *[[Media: | + | |
| − | + | ||
| + | The following datasets were analyzed in "GenGIS 2": | ||
| + | |||
| + | *[[Media:rca_tutorial.zip|RCA Tutorial]] containing the map, location, and sequence data for using the RCA plugin on the Upper Mersey data. | ||
Latest revision as of 23:17, 11 May 2017
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: RR1014):
- 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.
- Dispersal subtree of 16 complete S-OIV sequences demonstrating the rapid, global spread of S-OIV.
- Aneides Dataset containing sample files of Aneides Lugubris on the West Coast of the USA.
- Stream video showing the temporal and geographic spread of neuraminidase site N248D.
- Stream video showing the geophylogeny of a subtree exhibiting polymorphism at neuraminidase site 248.
The following datasets were analyzed in "GenGIS 2":
- RCA Tutorial containing the map, location, and sequence data for using the RCA plugin on the Upper Mersey data.
