Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses.

@article{Lanfear2012PartitionfinderCS,
  title={Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses.},
  author={Robert Lanfear and Brett Calcott and Simon Y. W. Ho and St{\'e}phane Guindon},
  journal={Molecular biology and evolution},
  year={2012},
  volume={29 6},
  pages={
          1695-701
        }
}
In phylogenetic analyses of molecular sequence data, partitioning involves estimating independent models of molecular evolution for different sets of sites in a sequence alignment. Choosing an appropriate partitioning scheme is an important step in most analyses because it can affect the accuracy of phylogenetic reconstruction. Despite this, partitioning schemes are often chosen without explicit statistical justification. Here, we describe two new objective methods for the combined selection of… 

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An Introduction to Supertree Construction (and Partitioned Phylogenetic Analyses) with a View Toward the Distinction Between Gene Trees and Species Trees

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...

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