https://github.com/4ment/aiv-migratory-flyways
https://github.com/4ment/aiv-migratory-flyways
data influenza
Last synced: 8 months ago
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- Host: GitHub
- URL: https://github.com/4ment/aiv-migratory-flyways
- Owner: 4ment
- Created: 2016-09-13T00:27:19.000Z (almost 10 years ago)
- Default Branch: master
- Last Pushed: 2017-05-26T10:16:54.000Z (about 9 years ago)
- Last Synced: 2024-12-27T04:42:26.122Z (over 1 year ago)
- Topics: data, influenza
- Language: Python
- Size: 3.58 MB
- Stars: 2
- Watchers: 3
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# The Impact of Migratory Flyways on the Spread of Avian Influenza Virus in North America
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](http://dx.doi.org/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:
* *countries.csv* contains the state/province to flyway assignment used in the study.
* *generate-models.py* is a python script that generates command line arguments on the standard output for reproducing the analyses using [_physher_](https://github.com/4ment/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