Publications by authors named "Sarah Lutteropp"
Bioinformatics
August 2022
Article Synopsis
- Phylogenetic networks are used to model complex evolutionary scenarios, but existing methods struggle with high computational demands and small datasets, especially when considering incomplete lineage sorting (ILS).
- The team introduces NetRAX, a maximum likelihood tool that simplifies network inference by avoiding ILS complications, utilizing efficient tree likelihood computations, and outputting results in Extended Newick format.
- NetRAX performs well on simulated data, providing accurate network inference quickly, and is available for use under an open-source license on GitHub.
Mol Biol Evol
February 2022
Article Synopsis
- Species tree inference from gene family trees is gaining popularity as it addresses differences between species trees and gene family trees, particularly using methods that handle multiple-copy gene families.
- The authors present SpeciesRax, a new maximum likelihood method that accurately infers rooted species trees while accounting for gene duplications, losses, and transfers.
- SpeciesRax demonstrates both high accuracy and speed, processing data from 188 vertebrate species in just one hour using 40 cores, and is available for public use on GitHub and BioConda.
Mol Ecol Resour
January 2022
Article Synopsis
- A variety of data types and computer tools exist for species delimitation (SD), but these methods are not commonly used by alpha-taxonomists due to challenges like lack of compatibility among different SD programs.
- Researchers often face time-consuming processes when comparing species partitions from different SD approaches due to their varying results and the absence of a standard format.
- The proposed standardized format, SPART, aims to improve compatibility among SD tools by reporting partitions and individual assignments, with options for including support values and original analysis details, while providing two user-friendly versions: matricial SPART and SPART.XML.
Article Synopsis
- Many daily publications focus on analyzing SARS-CoV-2 data, including phylogenetic studies available on nextstrain.org.
- The authors discuss challenges in creating reliable phylogenies due to a high number of virus sequences but a low number of mutations, making it tough to draw clear evolutionary connections.
- They conclude that while phylogenetic methods can offer some insights into COVID-19's evolution and spread, researchers should interpret results with caution, especially when using standard analysis tools.
Mol Ecol Resour
January 2021
Article Synopsis
- Microbial ecology research is advancing due to cheaper DNA sequencing and better data analysis methods, particularly through phylogenetic placement, which identifies unknown sequences based on a reference tree.
- A new tool called scrapp has been developed to analyze microbial diversity more effectively, utilizing a molecular species delimitation algorithm and a novel clustering approach to manage large data sets.
- Evaluation of scrapp with both simulated and real-world data shows it performs as well or better than existing methods in classifying samples based on diversity features, making it a valuable resource for researchers.
Bioinformatics
April 2020
Article Synopsis
- Researchers created a faster and more memory-efficient version of the transfer bootstrap expectation (TBE) method for phylogenetic analysis, addressing limitations of the original, resource-heavy tool.
- Their new implementation can be up to 480 times quicker and uses significantly less memory, making it better for large datasets.
- This optimized TBE method has been integrated into existing tools and is available for public use under an open-source license.
Article Synopsis
- - Incongruence in genome-scale data is a common issue, and new measures called internode certainty (IC) help quantify this problem in phylogenetic trees, offering a different approach than traditional statistical confidence measures.
- - Current IC score calculations struggle with missing taxa in genetic data, leading to inconsistent and often inflated estimates when relying on bipartition frequencies from partial trees.
- - We developed three new IC measures based on quartet frequencies, which perform better by being more consistent with data having missing taxa and demonstrating robustness against phylogenetic errors, with an open-source tool, QuartetScores, made available for researchers.
