smtools is my repository for molecular sequence manipulation tools and scripts related to genetic analysis. More tools may be added in the future.

• Simon Crameri (sfcrameri@gmail.com)

Please cite this page if you are using any of these tools for published work.

The bash script get.LSC.IR.SSC.from.chloroplast.genome.sh allows for excision of the three parts of plant chloroplast genomes: the large single-copy (LSC), small single-copy (SSC) and inverted repeat (IR) regions, respectively. The script takes advantage of the fact that most plant chloroplast genomes have two copies of the IR (leading to a quadripartite architecture, Jansen & Ruhlmann 2012), and that therefore, the boundaries between the LSC, IR and SSC can be easily determined using an alignment tool.

• Jansen RK, Ruhlman TA (2012) Plastid Genomes of Seed Plants. In: Genomics of Chloroplasts and Mitochondria: Advances in Photosynthesis and Respiration. Edited by Bock R, Knoop V, vol. 35: Springer Science and Business Media: 103–126.

The R script plot.simmatrix.R may be used within the DISSECT workflow (Jones et al 2015) for species delimitation. After running BEAST (Drummond et al 2012) or STACEY (Jones 2017) for BEAST2 (Bouckaert et al 2014) to obtain a set of species trees, one can "summarize the posterior frequencies of clusterings" using SpeciesDelimitationAnalyzer (speciesDA.jar, http://www.indriid.com/software.html). The similarity matrix can then be visualized using the R function plot.simmatrix, which is an extension on Graham Jones' version of the code (see http://www.indriid.com/2014/species-delim-paper-SuppIinfo-v8.pdf), and allows for automatic pairwise distance matrix sorting (using a summary tree topology in NEXUS format), labelling, and line drawing.

• Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu C-H, Xie D, Suchard, M.A., Rambaut A, Drummond A.J. (2014) BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Computational Biology, 10 (4), e1003537.
• Drummond, A.J. Marc A. Suchard, M.A., Xie D, Rambaut A (2012) Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution, 29, 1969–1973.
• Jones G, Zeynep A, Oxelman B (2015) DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent. Bioinformatics, 31(7), 991-998.
• Jones G (2017) Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent. Journal of Mathematical Biology, 74(1), 447-467.