https://github.com/4ment/aiv-migratory-flyways
Science Score: 26.0%
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Low similarity (6.0%) to scientific vocabulary
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Repository
Basic Info
- Host: GitHub
- Owner: 4ment
- Language: Python
- Default Branch: master
- Size: 3.58 MB
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- Stars: 2
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 1
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Metadata Files
README.md
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.
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. 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
Owner
- Name: Mathieu Fourment
- Login: 4ment
- Kind: user
- Location: Australia
- Company: University of Technology Sydney
- Repositories: 58
- Profile: https://github.com/4ment
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Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Mathieu Fourment | m****t@g****m | 3 |
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