worked_example.pdf

In this tutorial we will estimate the non-synonymous to synonymous rate ratio (ω = dN/dS) for 3,261 one-to-one orthologous gene alignments from six Plasmodium species (P. berghei: PB, P. chabaudi: PC, P. yoelii: PY, P. falciparum: PF, P. vivax: PV and P. knowlesii: PK), as well as performing some tests of adaptive evolution. The data are as described in (1). The files needed to run the tutorial are provided in the supplementary data file worked_example_files.zip. The sequence files are available at the PlasmoDB database (www.plasmodb.org), as described below. This tutorial assumes that you have some basic knowledge of working in a Unix system, and that you have PAML, Clustal Omega and PAL2NAL installed and working correctly. Please make sure you are working with the latest version of PAML (4.5 as of August 2012).