5 papers
Joint identifiability of ancestral sequence, phylogeny and mutation rates under the TKF91 model
Alex Xue, Brandon Legried, Wai-Tong Louis Fan
We consider the problem of identifying jointly the ancestral sequence, the phylogeny and the parameters in models of DNA sequence evolution with insertion and deletion (indel). Und…
Pairwise sequence alignment at arbitrarily large evolutionary distance
Brandon Legried, Sebastien Roch
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descenda…
Impossibility of phylogeny reconstruction from -mer counts
Wai-Tong Louis Fan, Brandon Legried, Sebastien Roch
We consider phylogeny estimation under a two-state model of sequence evolution by site substitution on a tree. In the asymptotic regime where the sequence lengths tend to infinity,…
Species tree estimation under joint modeling of coalescence and duplication: sample complexity of quartet methods
Max Hill, Brandon Legried, Sebastien Roch
We consider species tree estimation under a standard stochastic model of gene tree evolution that incorporates incomplete lineage sorting (as modeled by a coalescent process) and g…
Impossibility of consistent distance estimation from sequence lengths under the TKF91 model
Wai-Tong Louis Fan, Brandon Legried, Sebastien Roch
We consider the problem of distance estimation under the TKF91 model of sequence evolution by insertions, deletions and substitutions on a phylogeny. In an asymptotic regime where…