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Tree inference models

Jukes-Cantor

  • Model files: models/phylo/tree_inference.tppl, models/phylo/tree_inference_pruning.tppl, models/phylo/tree_inference_scaled.tppl

  • Example input data: models/phylo/tree_inference.json

  • Brief info: The model version tree_inference.tppl is a simple backwards tree reconstruction based on aligned DNA sequence data (converted to integers) as input, and using the Jukes-Cantor model of nucleotide substitution. There are also other and more computationally efficient model versions: tree_inference_pruning.tppl using hard-coded pruning (Felsenstein's pruning algorith) and tree_inference_scaled.tppl with pruning and a scaled approach to the messages. Use the scaled version for efficient inference on larger datasets.

GTR

  • Model file: models/phylo/tree_inference_pruning_gtr.tppl

  • Example input data: models/phylo/tree_inference.json

  • Brief info: The basic models using Jukes-Cantor above can easily be extended to adhere other models of nucleotide substitution. As an example, this is the GTR model with pruning.