Underline indicates Member of Molloy Lab
30.
29.
Leveraging constraints plus dynamic programming for the large Dollo parsimony problem
Dai, Rubel, Han, Molloy
WABI 2023
Dollo-CDP
28.
Fast, Parallel, and Cache-friendly Suffix Array Construction
Kahn, Rubel, Dhulipala, Molloy, Patro
WABI 2023
CaPS-SA
27.
26.
Improving quartet graph construction for scalable and accurate species tree estimation from gene trees
Han and Molloy
Genome Res / RECOMB 2023
TREE-QMC
25.
24.
23.
Theoretical and practical considerations when using retroelement insertions to estimate species trees in the anomaly zone
Molloy, Gatesy, Springer
Systematic Biology 2022
+
ASTRAL-BP MLE branch estimator
22.
Inferring population structure in biobank-scale genomic data
Chiu, Molloy, Tan, Talwalkar,
American J Human Genetics 2022
 
SCOPE
21.
Advancing admixture graph estimation via maximum likelihood network orientation
Molloy, Durvasula, Sankararaman
Bioinformatics / ISMB 2021
 
(and )
 
 
OrientAGraph
 
20.
19.
18.
TIPP2: Metagenomic taxonomic profiling using phylogenetic markers
Shah, Molloy, Pop, Warnow
Bioinformatics 2021
 
 
TIPP v2
17.
16.
ASTRAL-Pro: Quartet-based species tree inference despite paralogy
Zhang, Scornavacca, Molloy, Mirarab
Molecular Biology and Evolution 2020
 
 
ASTRAL-pro
15.
FastMulRFS: Fast and highly accurate species tree estimation under generic gene duplication and loss models
Molloy and Warnow
Bioinformatics / ISMB 2020
 
 
(and )
 
FastMulRFS
14.
ILS-Aware analysis of low-homoplasy retroelement insertions: Inference of species trees and introgression using quartets
Springer, Molloy, Sloan, Simmons, Gatesy
Journal of Heredity 2020
Editor's choice
 
 
ASTRAL-BP pipeline
13.
12.
TreeMerge: A new method for improving the scalability of species tree estimation methods
Molloy and Warnow
Bioinformatics / ISMB 2019
 
 
TreeMerge + pipeline
11.
Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge
Molloy and Warnow
Algorithms Mol Biol 2019 & RECOMB-CG 2018
 
 
NJMerge + pipeline
10.
9.
8.
7.
6.
5.
4.
3.
2.