Alignment-free phylogenetic reconstruction: Sample complexity via a branching process analysis
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Abstract: We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is distance-based, that is, it relies on pairwise sequence comparisons. More importantly, our approach largely bypasses the difficult problem of multiple sequence alignment.
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- Invertibility of the TKF model of sequence evolution
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- Maximal Accurate Forests from Distance Matrices
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Cited in
(21)- Identifiability of phylogenetic parameters from k-mer data under the coalescent
- An impossibility result for phylogeny reconstruction from \(k\)-mer counts
- Impossibility of consistent distance estimation from sequence lengths under the TKF91 model
- Statistically consistent and computationally efficient inference of ancestral DNA sequences in the TKF91 model under dense taxon sampling
- A note on probabilistic models over strings: the linear algebra approach
- A signal-to-noise analysis of phylogeny estimation by neighbor-joining: Insufficiency of polynomial length sequences
- Counting, Generating and Sampling Tree Alignments
- Phylogenies without branch bounds: contracting the short, pruning the deep
- Counting, Generating, Analyzing and Sampling Tree Alignments
- Predictive learning on hidden tree-structured Ising models
- Alignment- and reference-free phylogenomics with colored de Bruijn graphs
- Optimal sequence length requirements for phylogenetic tree reconstruction with indels
- Parametric analysis of alignment and phylogenetic uncertainty
- Comparative Genomics
- Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent
- Near-linear time edit distance for indel channels
- PhyBWT: alignment-free phylogeny via eBWT positional clustering
- Pairwise sequence alignment at arbitrarily large evolutionary distance
- Phase transition in the sample complexity of likelihood-based phylogeny inference
- Reconstructing ultrametric trees from noisy experiments
- Global alignment of molecular sequences via ancestral state reconstruction
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