isaacarvestad/pll-smc

A program which combines the methods of PosetSMC with the phylogenetic likelihood library

pll-smc

Sequential Monte Carlo phylogenetic tree inference using the PosetSMC algorithm with likelihood computations performed by the Phylogenetic Likelihood Library.

This project was written as a part of a bachelor thesis by Henrik Lagebrand and Isaac Arvestad, supervised by Jens Lagergren at KTH

Getting started

Instructions assume a Unix system with Bash or a similar shell.

Prerequisites

Before building, make sure the following is installed on your system:

• libpll
• CMake

Building

When in the root project directory:

mkdir build
cd build
cmake ..
make

This will build a runnable binary at [...]/pll-smc/build/app/pll-smc.

Usage

To run pll-smc, provide a path to a set of sequences in the Fasta format.

# Assuming inside 'build' directory
./app/pll-smc path/to/sequences.fasta

Optionally, the number of particles can be specified. If a value isn't provided default is 1000.

# Assuming inside 'build' directory
./app/pll-smc path/to/sequences.fasta 500

Once the tree distribution has been inferred it will be written to stdout. Progress information is written to stderr continuously during execution. To save the tree distribution we can redirect it to a file.

# Assuming inside 'build' directory
./app/pll-smc path/to/sequences.fasta > output.txt

Author

• Isaac Arvestad

Contributors

• Henrik Lagebrand

License

See license.