Computational protocol: Chikungunya Outbreak in Kedougou, Southeastern Senegal in 2009–2010

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Protocol publication

[…] Genome sequences representing the spatiotemporal distribution of CHIKV were downloaded from GenBank and aligned using MUSCLE [] and manually adjusted in Se-Al (available at http://tree.bio.ed.ac.uk/software/seal/) according to amino acid sequence homology. The E1 region was then excised and combined with the 34 newly generated CHIKV E1 sequences, leading to a final data set containing 103 sequences and 1317 nucleotides. A maximum likelihood tree was then inferred using the PAUP v4.0b package [], based on the best-fit nucleotide substitution model determined by MODELTEST []. The database and operation script is available upon request from the authors. […]

Pipeline specifications

Software tools MUSCLE, Se-Al, PAUP*, ModelTest-NG
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Homo sapiens, Human poliovirus 1 Mahoney
Diseases Chikungunya Fever