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 …
Inferring phylogenies from RAD sequence data
Reduced-representation genome sequencing represents a new source of data for
systematics, and its potential utility in interspecific phylogeny reconstruction has not yet been …
systematics, and its potential utility in interspecific phylogeny reconstruction has not yet been …
A genome tree of life for the fungi kingdom
JJ Choi, SH Kim - Proceedings of the National Academy of …, 2017 - National Acad Sciences
Fungi belong to one of the largest and most diverse kingdoms of living organisms. The
evolutionary kinship within a fungal population has so far been inferred mostly from the gene …
evolutionary kinship within a fungal population has so far been inferred mostly from the gene …
Evolution of modern birds revealed by mitogenomics: timing the radiation and origin of major orders
Mitochondrial (mt) genes and genomes are among the major sources of data for
evolutionary studies in birds. This places mitogenomic studies in birds at the core of intense …
evolutionary studies in birds. This places mitogenomic studies in birds at the core of intense …
[HTML][HTML] Plant phylogenomics based on genome-partitioning strategies: Progress and prospects
The rapid expansion of next-generation sequencing (NGS) has generated a powerful array
of approaches to address fundamental questions in biology. Several genome-partitioning …
of approaches to address fundamental questions in biology. Several genome-partitioning …
Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs)
GE Sims, SH Kim - Proceedings of the National Academy of …, 2011 - National Acad Sciences
A whole-genome phylogeny of the Escherichia coli/Shigella group was constructed by using
the feature frequency profile (FFP) method. This alignment-free approach uses the …
the feature frequency profile (FFP) method. This alignment-free approach uses the …
In the shadow of phylogenetic uncertainty: the recent diversification of Lysandra butterflies through chromosomal change
The phylogeny of the butterfly genus Lysandra (Lycaenidae, Polyommatinae) has been
intractable using both molecular and morphological characters, which could be a result of …
intractable using both molecular and morphological characters, which could be a result of …
Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer
The development of rapid, economical genome sequencing has shed new light on the
classification of viruses. As of October 2016, the National Center for Biotechnology …
classification of viruses. As of October 2016, the National Center for Biotechnology …
Spatially explicit models of dynamic histories: examination of the genetic consequences of Pleistocene glaciation and recent climate change on the American Pika
JL Brown, LL Knowles - Molecular Ecology, 2012 - Wiley Online Library
A central goal of phylogeography is to identify and characterize the processes underlying
divergence. One of the biggest impediments currently faced is how to capture the …
divergence. One of the biggest impediments currently faced is how to capture the …
K-mer natural vector and its application to the phylogenetic analysis of genetic sequences
Based on the well-known k-mer model, we propose a k-mer natural vector model for
representing a genetic sequence based on the numbers and distributions of k-mers in the …
representing a genetic sequence based on the numbers and distributions of k-mers in the …