Latest release: v1.7 - version history
With the PhylOStack a suite of phylogenetic software is easily installed using a series of installation scripts tailored for Linux Ubuntu 14.04. Cookbook instructions for using the software cover three basic steps: preparing input data, running an analysis and obtaining the output. The instructions are written for the Naturalis OpenStack cloud environment but should work in any cloud environment with AVX compatible hardware configuration.
Installation
Download and unpack or clone the repository and execute the install_all.sh script with:
bash /path/to/PhylOStack/install_all.sh
If this confuses you, try these instructions.
Cookbook instructions
- Create alignments with MAFFT
- Determine the right partitioning scheme and evolutionary model with PartitionFinder
- Bayesian inference of topologies with Exabayes
- Maximum likelihood estimations of topologies and rogue taxa pruning with RAxML and RogueNaRok
- Compare topologies with Dendextend
- Combine support values from two trees using the P4 combine support values script
- Collapse nodes in a tree below a set support value using the P4 collapse script
- Divergence time analyses with BEAST
- Divergence time analyses with PhyTime
- Bayesian diversification analyses with BAMM
- Combine multiple analyses in a single pipeline
- Multicore population structure analyses with Structure and the StrAuto python wrapper
Software suite: websites
Python based
- Miniconda2 ~1.6 GB
- ETE3 toolkit ~100 MB
- PartitionFinder v2 ~1 GB
- ipyrad v0.5.15
- P4 v1.2 ~200 MB
- StrAuto v1.0
R based
- R ~300 MB
- R Dendextend package
- R BAMMtools package
C++ or other languages
- RAxML v8 AVX2 PTHREADS ~80 MB
- MAFFT v7.273 ~10 MB
- Exabayes v1.5 AVX MPI-enabled ~200 MB
- RogueNaRok v1.0 ~20 MB
- BEAST v2.3.2 ~600 MB
- PhyML v2 20120412-2 ~20 MB
- BAMM v2.5 ~360 MB
- Structure v2.3.4