Alignment-free sequence comparison: benefits, applications, and tools
Alignment-free sequence analyses have been applied to problems ranging from whole-
genome phylogeny to the classification of protein families, identification of horizontally …
genome phylogeny to the classification of protein families, identification of horizontally …
Multiple genome alignment in the telomere-to-telomere assembly era
With the arrival of telomere-to-telomere (T2T) assemblies of the human genome comes the
computational challenge of efficiently and accurately constructing multiple genome …
computational challenge of efficiently and accurately constructing multiple genome …
Benchmarking of alignment-free sequence comparison methods
Background Alignment-free (AF) sequence comparison is attracting persistent interest driven
by data-intensive applications. Hence, many AF procedures have been proposed in recent …
by data-intensive applications. Hence, many AF procedures have been proposed in recent …
Skmer: assembly-free and alignment-free sample identification using genome skims
The ability to inexpensively describe taxonomic diversity is critical in this era of rapid climate
and biodiversity changes. The recent genome-skimming approach extends current …
and biodiversity changes. The recent genome-skimming approach extends current …
Alignment-free inference of hierarchical and reticulate phylogenomic relationships
We are amidst an ongoing flood of sequence data arising from the application of high-
throughput technologies, and a concomitant fundamental revision in our understanding of …
throughput technologies, and a concomitant fundamental revision in our understanding of …
[PDF][PDF] A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies
A Criscuolo - Research Ideas and Outcomes, 2019 - riojournal.com
This paper describes a novel alignment-free distance-based procedure for inferring
phylogenetic trees from genome contig sequences using publicly available bioinformatics …
phylogenetic trees from genome contig sequences using publicly available bioinformatics …
APPLES: scalable distance-based phylogenetic placement with or without alignments
Placing a new species on an existing phylogeny has increasing relevance to several
applications. Placement can be used to update phylogenies in a scalable fashion and can …
applications. Placement can be used to update phylogenies in a scalable fashion and can …
[HTML][HTML] On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference
A Criscuolo - F1000Research, 2020 - ncbi.nlm.nih.gov
Recently developed MinHash-based techniques were proven successful in quickly
estimating the level of similarity between large nucleotide sequences. This article discusses …
estimating the level of similarity between large nucleotide sequences. This article discusses …
The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances
S Röhling, A Linne, J Schellhorn, M Hosseini… - Plos one, 2020 - journals.plos.org
We study the number N k of length-k word matches between pairs of evolutionarily related
DNA sequences, as a function of k. We show that the Jukes-Cantor distance between two …
DNA sequences, as a function of k. We show that the Jukes-Cantor distance between two …
Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling
Computing distance between two genomes without alignments or even access to
assemblies has many downstream analyses. However, alignment-free methods, including in …
assemblies has many downstream analyses. However, alignment-free methods, including in …