H7 hemagglutinin lineage identification

This is the nucleotide sequence data and the R files for the k-means clustering of the H7 hemagglutinin segment of Influenza A. 

1. H7_HA_IRDB_2019_1_14.fasta is the initial data downloaded from the Influenza Research Database
2. H7_HA_IRDB_2019_1_14_aligned_muscle.fasta is the sequence data aligned with Muscle
3. H7_HA_IRDB_2019_1_14_aligned_muscle_cleaned.fas is the aligned sequence data after problem sequence have been removed.
4. RNA_distances_HA_kmeans_analysis.R is the R code for carrying out the k-means clustering and diagnostics.
5. kmeans_clustering.pdf is the R-markdown generated document describing the R-code for k-means clustering.
6. clustered_HA_kmeans_RNA.csv are the results of the clustering
7. usearch_clustering.csv is a summary of the USEARCH results.
8. Clade_Alpha.tree - alpha clade phylogenetic tree
9. Clade_Beta.tree - beta clade phylogenetic tree
10. Clade A-D trees are the phylogenetic trees for clades A to D.
11. H7_HA_IRDB_2019_1_14_aligned_muscle_cleaned_fasttree_coloured.tree is the overview tree of all the sequences.