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Computed_Data_2016-07-09.csv
Computed_Data_2016-08-26.csv
Location_Data_2016-05-27.csv
Makona_1610_cds_ig.GLM.MCC.tree
Makona_1610_genomes_2016-06-23.fasta
Makona_1610_genomes_2016-06-23.ml.tree
Makona_1610_metadata_2016-06-23.csv
Makona_1610_studies.csv
README.md
location_data_v3.geojson
phyml_raxml_ML.sh Adding Phyml/RAXML ML script Feb 18, 2017

README.md

space-time

Analysis of EBOV genome sequence from Guinea, Sierra Leone and Liberia from 2014-2016

Contents

Makona_1610_genomes_2016-06-23.fasta - a 1610 genome alignment in FASTA format. 'N's represent missing data from the individual data assemblies. Some putitive ADAR editing has been masked out (see manuscript for details) - these sites are marked with a '?' and were a 'C' in the original sequence. The first putitive edited site of a run is not masked to provide some phylogenetic signal.

Makona_1610_genomes_2016-06-23.ml.tree - a maximum likelihood phylogeny of the above data. Intended for data quality control and inspection.

Makona_1610_metadata_2016-06-23.csv - a table of available metadata for each sequence. Locations are prefectures/districts/counties for Guinea/Sierra Leone/Liberia, respectively with a '?' where this is unknown. Dates are usually dates of collection but in some cases these have been imputed by bracketting using sequentially labelled samples.

Location_Data_2016-05-27.csv - a table of data for each of the locations referenced in the sequence data set. These are data provided by Andy Tatem from a global GIS data set - references for this are to follow.

Metadata file - references for sequences:

Baize et al 2014 DOI: 10.1056/NEJMoa1404505

Gire et al 2014 DOI: 10.1126/science.1259657 PMID: 25214632

Tong et al 2015 DOI: 10.1038/nature14490

Carroll et al 2015 DOI: 10.1038/nature14594

Park et al 2015 DOI: 10.1016/j.cell.2015.06.007

Simon-Loriere et al 2015 DOI: 10.1038/nature14612

Hoenen et al 2015 DOI: 10.1126/science.aaa5646

Ladner et al 2015 DOI: 10.1016/j.chom.2015.11.008

Kugelman et al 2015 DOI: 10.3201/eid2107.150522

Bell et al 2015 DOI: 10.2807/1560-7917.ES2015.20.20.21131

Smits et al 2015 DOI: 10.2807/1560-7917.ES.2015.20.40.30035

Quick et al 2016 DOI: 10.1038/nature16996

Arias et al 2016 DOI: 10.1093/ve/vew016

The others are as yet unpublished. See GenBank entries for author contact details.

License

The contents of this project are licensed under the Creative Commons Attribution 4.0 license with the exception of source code which may be under other individual licences.

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