Hi there,
I would hazard a guess that your cluster issue is due to the fact that HyPhy (by default) expects to find its library files in /usr/local/lib/hyphy
Please check to see where the "TemplateBatchFiles" directory lives on the cluster, or use the build-time options (README Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to
) to have HyPhy install somewhere else. Also, if you are using a queueing system (e.g. SGE or torque), it may only copy the HyPhy binary to the remote (compute) nodes. In this case, you may need to modify your job submission files to also "bring along" all the libraries that HyPhy has.
In terms of finding sites under episodic selection, we have an upcoming paper in PLoS Genetics (preprint attached), which describes the MEME method for doing this. The paper contains is a pertinent quote that I would like to draw your attention to:
Quote:The ability of MEME, or similar substitution model-based methods, to accurately infer the identity of individual branches subject to diversifying selection at a given site seems unavoidably limited. Most of the information that such inference might be based on is limited to character substitutions along a single branch at a single site, i.e. one realization of the Markov substitution process. Selection along terminal branches in the context of negatively selected background can be detected more reliably than selection along interior branches among neutrally evolving background lineages. However, we caution that despite obvious interest in identifying specific branch-site combinations subject to diversifying selection, such inference is based on very limited data (the evolution of one codon along one branch), and cannot be recommended for purposes other than data exploration and result visualization. This observation could be codified as the “selection inference uncertainty principle” – one cannot simultaneously infer both the site and the branch subject to diversifying selection. In this manuscript, we describe how to infer the location of sites, pooling information over branches; previously [20] we have outlined a complementary approach to find selected branches by pooling information over sites.
Sergei