AbstractMotivationWith the recent breakthroughs in sequencing technology, phylogeny estimation at a larger scale has become a huge opportunity. For accurate estimation of large-scale phylogeny, substantial endeavor is being devoted in introducing new algorithms or upgrading current approaches. In this work, we endeavor to improve the Quartet Fiduccia and Mattheyses (QFM) algorithm to resolve phylogenetic trees of better quality with better running time. QFM was already being appreciated by researchers for its good tree quality, but fell short in larger phylogenomic studies due to its excessively slow running time.ResultsWe have re-designed QFM so that it can amalgamate millions of quartets over thousands of taxa into a species tree with a great level of accuracy within a short amount of time. Named “QFM Fast and Improved (QFM-FI)”, our version is 20 000× faster than the previous version and 400× faster than the widely used variant of QFM implemented in PAUP* on larger datasets. We have also provided a theoretical analysis of the running time and memory requirements of QFM-FI. We have conducted a comparative study of QFM-FI with other state-of-the-art phylogeny reconstruction methods, such as QFM, QMC, wQMC, wQFM, and ASTRAL, on simulated as well as real biological datasets. Our results show that QFM-FI improves on the running time and tree quality of QFM and produces trees that are comparable with state-of-the-art methods.Availability and implementationQFM-FI is open source and available athttps://github.com/sharmin-mim/qfm_java.