Information theoretic generalized Robinson–Foulds metrics for comparing phylogenetic trees
MR Smith - Bioinformatics, 2020 - academic.oup.com
Abstract Motivation The Robinson–Foulds (RF) metric is widely used by biologists, linguists
and chemists to quantify similarity between pairs of phylogenetic trees. The measure tallies …
and chemists to quantify similarity between pairs of phylogenetic trees. The measure tallies …
[HTML][HTML] The era of the ARG: an empiricist's guide to ancestral recombination graphs
In the presence of recombination, the evolutionary relationships between a set of sampled
genomes cannot be described by a single genealogical tree. Instead, the genomes are …
genomes cannot be described by a single genealogical tree. Instead, the genomes are …
Robust analysis of phylogenetic tree space
MR Smith - Systematic Biology, 2022 - academic.oup.com
Phylogenetic analyses often produce large numbers of trees. Mapping trees' distribution in
“tree space” can illuminate the behavior and performance of search strategies, reveal …
“tree space” can illuminate the behavior and performance of search strategies, reveal …
Sage Insights Into the Phylogeny of Salvia: Dealing With Sources of Discordance Within and Across Genomes
Next-generation sequencing technologies have facilitated new phylogenomic approaches to
help clarify previously intractable relationships while simultaneously highlighting the …
help clarify previously intractable relationships while simultaneously highlighting the …
Species-specific traits mediate avian demographic responses under past climate change
Anticipating species' responses to environmental change is a pressing mission in
biodiversity conservation. Despite decades of research investigating how climate change …
biodiversity conservation. Despite decades of research investigating how climate change …
The history, systematics, and nomenclature of Thalattosuchia (Archosauria: Crocodylomorpha)
The use of more than one nomenclatural code is becoming increasingly common in some
biological sub-disciplines. To minimize nomenclatural instability, we have decided to …
biological sub-disciplines. To minimize nomenclatural instability, we have decided to …
Phylogenetic signal and bias in paleontology
An unprecedented amount of evidence now illuminates the phylogeny of living mammals
and birds on the Tree of Life. We use this tree to measure the phylogenetic value of data …
and birds on the Tree of Life. We use this tree to measure the phylogenetic value of data …
Machine learning based lineage tree reconstruction improved with knowledge of higher level relationships between cells and genomic barcodes
A Prusokiene, A Prusokas… - NAR Genomics and …, 2023 - academic.oup.com
Tracking cells as they divide and progress through differentiation is a fundamental step in
understanding many biological processes, such as the development of organisms and …
understanding many biological processes, such as the development of organisms and …
rphenoscate: An R package for semantics‐aware evolutionary analyses of anatomical traits
Organismal anatomy is a hierarchical system of anatomical entities often imposing
dependencies among multiple morphological characters. Ontologies provide a formal and …
dependencies among multiple morphological characters. Ontologies provide a formal and …
The Cambrian cirratuliform Iotuba denotes an early annelid radiation
ZF Zhang, MR Smith, XY Ren - Proceedings of the …, 2023 - royalsocietypublishing.org
The principal animal lineages (phyla) diverged in the Cambrian, but most diversity at lower
taxonomic ranks arose more gradually over the subsequent 500 Myr. Annelid worms seem …
taxonomic ranks arose more gradually over the subsequent 500 Myr. Annelid worms seem …