A-pro

ASTRAL for PaRalogs and Orthologs

Required installations

• Java (>=1.7)

• If you need to compile (you may not), you will also need JDK and g++ or icc (supporting c++11 standard)

Installation

Normally, you would not need to install. You can just run A-Pro, as we show bellow.

If you have trouble with running the packaged A-Pro,

1. cd ASTRAL-MP
2. bash make.sh.

For more information please see AVX2 section of https://github.com/smirarab/ASTRAL/tree/MP

Input requirement

The input gene trees must be in the Newick format, either multi-labelled (eg. ((SpeciesA,SpeciesB),(SpeciesA,SpeciesC));) or with gene-name-to-species-name mapping provided in the following format (eg. for ((GeneA1,GeneB1),(GeneA2,GeneC1));):

GeneA1 SpeciesA
GeneA2 SpeciesA
GeneB1 SpeciesB
GeneC1 SpeciesC

Running A-pro

cd to ASTRAL-MP and run for multi-labelled gene trees:

java -D"java.library.path=lib" -jar astral.<version_number>.jar -i input -o output

cd to ASTRAL-MP and run for gene trees with gene-name-to-species-name mapping provided:

java -D"java.library.path=lib" -jar astral.<version_number>.jar -i input -a mapping -o output

Note that instead of cd to ASTRAL-MP, you can replace astral.<version_number>.jar and -D"java.library.path=lib/" with absolute path to A-Pro. For example, if my A-Pro is located on /Users/smirarab/A-pro, you can use:

java -D"java.library.path=/Users/smirarab/A-pro/lib" -jar /Users/smirarab/A-pro/astral.<version_number>.jar -i input -o output