Curated list of citations relevant to PartitionFinder by Rob Lanfear

PartitionFinder_Citations.md

PartitionFinder Citations

v1.1.0 manual:

• Lanfear, R., 2013. PartitionFinder v1.1.0 and PartitionFinderProtein v1.1.0 Manual. Available from: http://www.robertlanfear.com/partitionfinder.

v1.1.0 software:

• Lanfear, R., Calcott, B., Ho, S.Y. and Guindon, S., 2012. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution, 29(6), 1695-1701.

v2 manual:

• Lanfear, R., 2016. PartitionFinder 2 Manual. Available from: http://www.robertlanfear.com/partitionfinder.

v2 software:

• Lanfear, R., Frandsen, P.B., Wright, A.M., Senfeld, T. and Calcott, B., 2017. PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular Biology and Evolution 34(3), 772–773. DOI: dx.doi.org/10.1093/molbev/msw260.

rcluster and hcluster algorithms:

• Lanfear, R., Calcott, B., Kainer, D., Mayer, C., & Stamatakis, A. (2014). Selecting optimal partitioning schemes for phylogenomic datasets. BMC Evolutionary Biology, 14(1), 82.

PhyML:

• Guindon, S., Dufayard, J.F., Lefort, V., Anisimova, M., Hordijk, W. and Gascuel, O., 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic biology, 59(3), pp.307-321.

RAxML (v8+):

• Stamatakis, A., 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics, 30(9), 1312-1313.

RAxML (original):

• Stamatakis, A., 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22(21), 2688-2690.