Phylogenetics Overview

DECIPHER offers a rich feature set for performing phylogenetic analyses. The two workhorse functions for phylogenetics are DistanceMatrix and Treeline.

Why use DECIPHER for phylogenetics?

• Treeline can optimize trees for multiple objectives within a single function, facillitating comparison across different criteria.
• Many different nucleotide and amino acid models of evolution are supported, including automatic model selection by likelihood.
• Treeline is accurate and fast, with excellent time and memory scalability.
• DECIPHER contains tools for other phylogenetic analyses, including ancestral state reconstruction and mapping character state changes.

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Minimum Evolution (ME) Trees - Minimize (balanced) tree length given a distance matrix derived from a sequence alignment and a model of evolution.

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Maximum Likelihood (ML) Trees - Maximize the likelihood of the tree given an alignment and a model of evolution.

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Maximum Parsimony (MP) Trees - Maximize the parsimony score of a tree according to a cost matrix.

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Ancestral State Reconstruction - Estimate the ancestral sequence states at each internal node on a phylogeny and map state changes along each branch.