Workflow for Phylogenetic Analysis using the Swift parallel scripting system.
Reference: Ocaña, Kary ACS, et al. "Sciphy: A cloud-based workflow for phylogenetic analysis of drug targets in protozoan genomes." Advances in Bioinformatics and Computational Biology. Springer Berlin Heidelberg, 2011. 66-70.
This uses the tools:
- mafft: http://mafft.cbrc.jp/alignment/software/
- raxml: http://sco.h-its.org/exelixis/web/software/raxml/index.html
- Swift: http://swift-lang.org/main/ (installation guide, documentation, downloads and general information about the Swift parallel scripting language)
- Python (version => 2.5)
You can install the required programs and scripts from swift-phylo by running:
sudo apt-get update sudo apt-get install raxml sudo apt-get install mafft export SWIFT_PHYLO=/path/to/swift-phylo/bin export PATH=$SWIFT_PHYLO:$PATH
Run the following command in the directory where the input files are placed:
swift -config swift.conf swiftPhylo.swift
The other binaries/applications needed to execute the workflow are in the /bin directory of this repository. For Swift to recognize them as executable programs, it is necessary to add this directory to the system path:
export PATH=<path to /bin>:$PATH