Phylogenomic resolution of the root of Panpulmonata, a hyperdiverse radiation of gastropods: new insight into the evolution of air breathing
PJ Krug, SA Caplins, K Algoso… - … of the Royal …, 2022 - royalsocietypublishing.org
Transitions to terrestriality have been associated with major animal radiations including land
snails and slugs in Stylommatophora (> 20 000 described species), the most successful …
snails and slugs in Stylommatophora (> 20 000 described species), the most successful …
Recent progress on methods for estimating and updating large phylogenies
P Zaharias, T Warnow - Philosophical Transactions of the …, 2022 - royalsocietypublishing.org
With the increased availability of sequence data and even of fully sequenced and
assembled genomes, phylogeny estimation of very large trees (even of hundreds of …
assembled genomes, phylogeny estimation of very large trees (even of hundreds of …
Improving quartet graph construction for scalable and accurate species tree estimation from gene trees
Summary methods are widely used to estimate species trees from genome-scale data.
However, they can fail to produce accurate species trees when the input gene trees are …
However, they can fail to produce accurate species trees when the input gene trees are …
Weighted ASTRID: fast and accurate species trees from weighted internode distances
Background Species tree estimation is a basic step in many biological research projects, but
is complicated by the fact that gene trees can differ from the species tree due to processes …
is complicated by the fact that gene trees can differ from the species tree due to processes …
A Guide to Phylogenomic Inference
JSL Patané, J Martins Jr, JC Setubal - Comparative Genomics: Methods …, 2024 - Springer
Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into
account whole genomes or large fractions of genomes. Phylogenomics has significant …
account whole genomes or large fractions of genomes. Phylogenomics has significant …
[PDF][PDF] Using all gene families vastly expands data available for phylogenomic inference
ML Smith, D Vanderpool… - Molecular Biology and …, 2022 - academic.oup.com
Traditionally, single-copy orthologs have been the gold standard in phylogenomics. Most
phylogenomic studies identify putative single-copy orthologs using clustering approaches …
phylogenomic studies identify putative single-copy orthologs using clustering approaches …
Leveraging Constraints plus dynamic programming for the large dollo parsimony problem
The last decade of phylogenetics has seen the development of many methods that leverage
constraints plus dynamic programming. The goal of this algorithmic technique is to produce …
constraints plus dynamic programming. The goal of this algorithmic technique is to produce …
Dollo-CDP: a polynomial-time algorithm for the clade-constrained large Dollo parsimony problem
The last decade of phylogenetics has seen the development of many methods that leverage
constraints plus dynamic programming. The goal of this algorithmic technique is to produce …
constraints plus dynamic programming. The goal of this algorithmic technique is to produce …
Scalable species tree inference with external constraints
Species tree inference is a basic step in biological discovery, but discordance between gene
trees creates analytical challenges and large data sets create computational challenges …
trees creates analytical challenges and large data sets create computational challenges …
Quartets enable statistically consistent estimation of cell lineage trees under an unbiased error and missingness model
Cancer progression and treatment can be informed by reconstructing its evolutionary history
from tumor cells. Although many methods exist to estimate evolutionary trees (called …
from tumor cells. Although many methods exist to estimate evolutionary trees (called …