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BACKGROUND: We recently described FastTree, a tool for inferring phylogenies for alignments with up to hundreds of thousands of sequences. Here, we describe improvements to FastTree that improve its accuracy without sacr...

We are given a large database of customer transactions. Each transaction consists of items purchased by a customer in a visit. We present an efficient algorithm that generates all significant association rules between it...

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the origi...

The purpose of this study is to introduce new design-criteria for next-generation hyperparameter optimization software. The criteria we propose include (1) define-by-run API that allows users to construct the parameter s...

Motivation: Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter tri...