Rearrangements in Phylogenetic Inference: Compare, Model, or Encode?

DOI10.1007/978-1-4471-5298-9_7zbMath1462.92042OpenAlexW2293111751MaRDI QIDQ4992757

Bernard M. E. Moret, Yu Lin, Jijun Tang

Publication date: 10 June 2021

Published in: Models and Algorithms for Genome Evolution (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1007/978-1-4471-5298-9_7

zbMATH Keywords

edit distancemaximum parsimonybinary sequencephylogenetic inferencetrue distance

Mathematics Subject Classification ID

Problems related to evolution (92D15) Genetics and epigenetics (92D10)

Uses Software

• RAxML
• GRAPPA
• FastTree
• GASTS

Cites Work

• A new linear time algorithm to compute the genomic distance via the double cut and join distance
• Probabilistic models of genome shuffling
• High-performance algorithm engineering for computational phylogenetics
• Comparative genomics. Empirical and analytical approaches to gene order dynamics, map alignment and the evolution of gene families. Papers at the DCAF workshop, Québec, Canada, September 22--25, 2000
• Steps toward accurate reconstructions of phylogenies from gene-order data.
• Efficient algorithms for multichromosomal genome rearrangements.
• Genomic distances under deletions and insertions
• Genome rearrangements: a correct algorithm for optimal capping
• Sorting by Transpositions Is Difficult
• Minimal Mutation Trees of Sequences
• Bayesian Phylogenetic Inference from Animal Mitochondrial Genome Arrangements
• The Reconstruction of Doubled Genomes
• Exact-IEBP: A New Technique for Estimating Evolutionary Distances between Whole Genomes
• Finding an Optimal Inversion Median: Experimental Results
• On the Practical Solution of the Reversal Median Problem
• Estimating true evolutionary distances between genomes
• Approximating the true evolutionary distance between two genomes
• Research in Computational Molecular Biology
• Combinatorial Pattern Matching
• Conserved synteny as a measure of genomic distance
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