Analysis of EBOV genome sequence from Guinea, Sierra Leone and Liberia from 2014-2016
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The others are as yet unpublished.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.
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.