African Horse Sickness Virus


African Horse Sickness sequences were downloaded from GenBank on 25th Oct 2013.
Initial processing to split the sequences into separate files according to segment was performed using a custom R script epic_process_background_seqs_african_horse_sickness.R, followed by manual editting of the sequence files.

Nucleotide sequences (fasta format) were manually inspected and translated to amino acids for alignment using MUSCLE in MEGA 5.

Neighbour joining trees (newick format) were created in MEGA with the TN93 model, pairwise deletetion, and heterogenous rates between sites and lineages.

Segment and protein information from Roy et al 1994

All sequences with original full names as zip file

Table 1: Individual segments with original full names
SegmentLengthProteinLocationFASTANum.Seqs.NJ Tree
L1 3500 VP1 core segment 1 7 NJ Tree
L2 3229 VP2 outer shell segment 2 55 See individual serotype files
L3 2792 VP3 core segment 3 22 NJ Tree
M4 1978 VP4 core segment 4 21 NJ Tree
M5 1751 NS1 non-structural segment 5 63 NJ Tree
M6 1566 VP5 outer shell segment 6 32 NJ Tree
S7 1179 VP7 core segment 7 56 NJ Tree
S8 116 NS2 non-structural segment 8 44 NJ Tree
S9 1100 VP6 core segment 9 7 NJ Tree
S10 756 NS3/3A non-structural segment 10 205 NJ Tree

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