PhyloFusion- Fast and easy fusion of rooted phylogenetic trees into rooted phylogenetic networks [0.03%]
PhyloFusion-快速且简单的将有根的系统发生树融合为有根的系统发育网络
Louxin Zhang,Banu Cetinkaya,Daniel H Huson
Louxin Zhang
Unrooted phylogenetic networks are commonly used to represent evolutionary data in the presence of incompatibilities. While rooted phylogenetic networks offer a more explicit framework for depicting evolutionary histories involving reticula...
Revisiting the Multispecies Coalescent Model fit with an example from a complete molecular phylogeny of the Liolaemus wiegmannii species group (Squamata: Liolaemidae) [0.03%]
利用Liolaemus wiegmannii种组(石龙子目：Liolaemida科)完整分子系统发育树重新研究多物种溯祖模型拟合性
Joaquín Villamil,Mariana Morando,Luciano J Avila et al.
Joaquín Villamil et al.
Departures from the Multispecies Coalescent (MSC) assumptions could cause artefactual topologies and node height estimates, and therefore, trees inferred without MSC model fit testing could potentially misrepresent an accurate approximation...
torchtree: flexible phylogenetic model development and inference using PyTorch [0.03%]
TorchTree：使用PyTorch灵活的生成模型开发和推理
Mathieu Fourment,Matthew Macaulay,Christiaan J Swanepoel et al.
Mathieu Fourment et al.
Bayesian inference has predominantly relied on the Markov chain Monte Carlo (MCMC) algorithm for many years. However, MCMC is computationally laborious, especially for complex phylogenetic models of time trees. This bottleneck has led to th...
Ana Serra Silva,Karen Siu-Ting,Christopher J Creevey et al.
Ana Serra Silva et al.
Missing data is a long standing issue in phylogenetic inference, which often results in high levels of taxonomic instability, obscuring otherwise well supported relationships. Multiple approaches have been developed to deal with the negativ...
The explosive radiation of the Neotropical Tillandsia subgenus Tillandsia (Bromeliaceae) has been accompanied by pervasive hybridization [0.03%]
辐射构造革叶铁兰亚属（凤梨科）的爆发伴随着广泛的杂交现象
Gil Yardeni,Michael H J Barfuss,Walter Till et al.
Gil Yardeni et al.
The recent rapid radiation of Tillandsia subgenus Tillandsia (Bromeliaceae) provides an attractive system to study the drivers and constraints of species diversification. This species-rich Neotropical monocot clade includes predominantly ep...
Lara M Ko Sters,Kevin Karbstein,Martin Hofmann et al.
Lara M Ko Sters et al.
DNA analyses have revolutionized species identification and taxonomic work. Yet, persistent challenges arise from little differentiation among and considerable variation within species, particularly among closely related groups. While image...
Link between the Birth-Death process and the Kingman Coalescent - Applications to Phylogenetic Epidemiology [0.03%]
birth-death过程与Kingman coalescent之间的关系及其在系谱流行病学中的应用
Josselin Cornuault,Fabio Pardi,Celine Scornavacca
Josselin Cornuault
The two most popular tree models used in phylogenetics are the birth-death process (BD) and the Kingman coalescent (KC). These two models differ in several respects, notably: (i) the curve of the population size through time is a stochastic...
Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping to Evade (Over-)optimization [0.03%]
通过提前停止以避免过度优化来加速最大似然法的系统发育推断
Anastasis Togkousidis,Alexandros Stamatakis,Olivier Gascuel
Anastasis Togkousidis
Maximum Likelihood (ML) based phylogenetic inference constitutes a challenging optimization problem. Given a set of aligned input sequences, phylogenetic inference tools strive to determine the tree topology, the branch-lengths, and the evo...
Phylogenetic Estimation of Branch-specific Shifts in the Tempo of Origination [0.03%]
分支特异性起源速率变化的谱系地质估计
Bjørn T Kopperud,Sebastian Höhna
Bjørn T Kopperud
Studying rates of species diversification is one of the key themes in macroevolution. In particular, we are interested in if some clades in a phylogeny diversify more rapidly/slowly than others due to branch-specific diversification rates. ...