A fast algorithm for joint reconstruction of ancestral amino acid sequences

Research output: Contribution to journalArticlepeer-review

Abstract

A dynamic programming algorithm is developed for maximum-likelihood reconstruction of the set of all ancestral amino acid sequences in a phylogenetic tree. To date, exhaustive algorithms that find the most likely set of ancestral states (joint reconstruction) have running times that scale exponentially with the number of sequences and are thus limited to very few taxa. The time requirement of our new algorithm scales linearly with the number of sequences and is therefore applicable to practically any number of taxa. A detailed description of the new algorithm and an example of its application to cytochrome b sequences are provided.

Original languageEnglish
Pages (from-to)890-896
Number of pages7
JournalMolecular Biology and Evolution
Volume17
Issue number6
DOIs
StatePublished - Jun 2000

Keywords

  • Ancestral sequences
  • Dynamic programming
  • Fast algorithm
  • Joint reconstruction
  • Maximum likelihood
  • Molecular evolution

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