This hands-on workshop will introduce users of the R software environment to the techniques involved in generating reproducible, dynamic data analyses and reports. Using literate programming approaches, participants will learn to build automated reusable reports in R.
Lateral Genetic Transfer Pipeline
Lateral Genetic transfer (LGT) involves the movement of genetic material from one lineage into another and its subsequent incorporation into the new host genome via genetic recombination. Studies in individual taxa have indicated lateral origins for stretches of DNA.
QFAB has implemented a two-phase approach strategy pipeline for this study.
In the first phase, Phipack is used to detect the occurrences of recombination based on divergence of phylogenetic signal within the sequence alignments. In the second phase, for each sequence set that showed evidence of recombination, a Bayesian phylogenetic approach was used to define recombination breakpoints. This was implemented in DualBrothers and run with Markov chain Monte Carlo. The tree search space for each run of Dualbrothers was defined by a list of tree topologies using MrBayes.
This second step is computationally expensive in time and memory. To reduce these issues, the Pipeline has been deployed on the QFAB Cluster.
Finally, the posterior output of DualBrothers is then used to identify gene sets exhibiting evidence of within-gene transfers.