This repository contains the data sets supporting the results of the following article:
Fourment M, Darling AE, and Holmes EC The Impact of Migratory Flyways on the Spread of Avian Influenza Virus in North America. BMC Evolutionary Biology, 2017, 17:118; DOI: 10.1186/s12862-017-0965-4.
Data sets are organised by gene (i.e. PB2, PB1, PA, NP, and MP) and each folder contains:
- a fasta file containing the nucleotide alignment (*-dna.fa)
- a tree file inferred from the nucleotide alignment (*.tree)
- a fasta file containing the geographic location of each sequence (*-geo.fa)
Other files:
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countries.csv contains the state/province to flyway assignment used in the study.
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generate-models.py is a python script that generates command line arguments on the standard output for reproducing the analyses using physher. For each genes it will generate the command line arguments for:
- HRM: homogeneous rate model
- 3-TRM: two-rate model with 3 flyways (Pacific, Central/Mississippi, and Atlantic)
- 4-TRM: two-rate model with 4 flyways (Pacific, Central, Mississippi, and Atlantic)
- 3-FRM: flyway-based model with 3 flyways
- 4-FRM: flyway-based model with 4 flyways
- Best model found by the genetic algorithm