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 …
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 …
The transcriptome of Balamuthia mandrillaris trophozoites for structure-guided drug design
Balamuthia mandrillaris, a pathogenic free-living amoeba, causes cutaneous skin lesions as
well as granulomatous amoebic encephalitis, a 'brain-eating'disease. As with the other …
well as granulomatous amoebic encephalitis, a 'brain-eating'disease. As with the other …
De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y …
A Bayega, H Djambazian, KT Tsoumani, ME Gregoriou… - BMC genomics, 2020 - Springer
Background The olive fruit fly, Bactrocera oleae, is the most important pest in the olive fruit
agribusiness industry. This is because female flies lay their eggs in the unripe fruits and …
agribusiness industry. This is because female flies lay their eggs in the unripe fruits and …
Phylogenies from unaligned proteomes using sequence environments of amino acid residues
JC Aledo - Scientific reports, 2022 - nature.com
Alignment-free methods for sequence comparison and phylogeny inference have attracted a
great deal of attention in recent years. Several algorithms have been implemented in diverse …
great deal of attention in recent years. Several algorithms have been implemented in diverse …
Read-SpaM: assembly-free and alignment-free comparison of bacterial genomes with low sequencing coverage
AK Lau, S Dörrer, CA Leimeister, C Bleidorn… - BMC …, 2019 - Springer
Background In many fields of biomedical research, it is important to estimate phylogenetic
distances between taxa based on low-coverage sequencing reads. Major applications are …
distances between taxa based on low-coverage sequencing reads. Major applications are …
Evolutionary insight into the Trypanosomatidae using alignment-free phylogenomics of the kinetoplast
Advancements in next-generation sequencing techniques have led to a substantial increase
in the genomic information available for analyses in evolutionary biology. As such, this data …
in the genomic information available for analyses in evolutionary biology. As such, this data …
CGRWDL: alignment-free phylogeny reconstruction method for viruses based on chaos game representation weighted by dynamical language model
T Wang, ZG Yu, J Li - Frontiers in Microbiology, 2024 - frontiersin.org
Traditional alignment-based methods meet serious challenges in genome sequence
comparison and phylogeny reconstruction due to their high computational complexity. Here …
comparison and phylogeny reconstruction due to their high computational complexity. Here …
'Multi-SpaM': a maximum-likelihood approach to phylogeny reconstruction using multiple spaced-word matches and quartet trees
Word-based or 'alignment-free'methods for phylogeny inference have become popular in
recent years. These methods are much faster than traditional, alignment-based approaches …
recent years. These methods are much faster than traditional, alignment-based approaches …
Mottle: Accurate pairwise substitution distance at high divergence through the exploitation of short-read mappers and gradient descent
Current tools for estimating the substitution distance between two related sequences
struggle to remain accurate at a high divergence. Difficulties at distant homologies, such as …
struggle to remain accurate at a high divergence. Difficulties at distant homologies, such as …