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Biorxiv : the Preprint Server for Biology|April 27, 2026
Phlag: Scalable detection of genomics regions with unexplained phylogenetic heterogeneityAli Osman Berk Şapcı, Shayesteh Arasti, Edward L Braun, et al.Bioinformatics (Oxford, England)|July 7, 2026
Phlag: scalable detection of genomics regions with unexplained phylogenetic heterogeneityAli Osman Berk Şapcı, Shayesteh Arasti, Edward L Braun, et al.Genome Biology|February 15, 2019
Skmer: assembly-free and alignment-free sample identification using genome skimsShahab Sarmashghi, Kristine Bohmann, M Thomas P Gilbert, et al.Journal of Computational Biology : a Journal of Computational Molecular Cell Biology|December 31, 2014
PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid SequencesSiavash Mirarab, Nam Nguyen, Sheng Guo, et al.Biorxiv : the Preprint Server for Biology|February 6, 2026
Deconvolving Phylogenetic Distance MixturesShayesteh Arasti, Ali Osman Berk Şapcı, Eleonora Rachtman, et al.Algorithms for Molecular Biology : AMB|June 1, 2017
The gene family-free median of threeDaniel Doerr, Metin Balaban, Pedro Feijão, et al.BMC Genomics|October 10, 2015
A comparative study of SVDquartets and other coalescent-based species tree estimation methodsJed Chou, Ashu Gupta, Shashank Yaduvanshi, et al.Nature Methods|February 20, 2018
Identifying the favored mutation in a positive selective sweepAli Akbari, Joseph J Vitti, Arya Iranmehr, et al.Genome Biology|May 23, 2026
ReSkmer: modeling repeats allows k-mer-based alignment-free methods to calculate population genomic distancesEduardo Charvel, Isaac Thomas, Homère J Alves Monteiro, et al.Nature Biotechnology|July 27, 2023
Greengenes2 unifies microbial data in a single reference treeDaniel McDonald, Yueyu Jiang, Metin Balaban, et al.Pageof 12