This software is intended for the inference of Ancestral Alleles (AA) using a whole-genome multiple alignment.

perl run_aa.pl --emf EMF_DIR --input INPUT.txt --output OUTPUT.txt

This will go through all the variants in the INPUT.txt file and calculates the AA for each of them. At the moment only a specific TSV file format is supported, but new file format (notably VCF will be supported in the near future).

• Ortheus: https://github.com/benedictpaten/ortheus, although https://github.com/jherrero/ortheus/tree/original-code is recommended
• Muscle: http://www.drive5.com/muscle/

Much has chenged since the previous verisons, but this is largely inspired by the work done by Kathryn Beal while at the European Bioinformatics Institute (http://www.ebi.ac.uk). This was done under the supervision of Javier Herrero, in Paul Flicek's group.

The original files can be found in the Ensembl Compara repository, under modules/Bio/EnsEMBL/Compara/RunnableDB/AncestralAllelesForIndels