QuickTree: building huge Neighbour-Joining trees of protein sequences

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Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge (2009, methodology): “The software Quicktree (Howe et al., 2002) was used to build the general trees for Bacteria and Archaea domains.”
The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database (2017, methodology): “An alignment is made from the sequence library using MUSCLE (12) and a phylogenetic tree is made from the alignment using the UPGMA method of QuickTree (13).”
bold: The Barcode of Life Data System (http://www.barcodinglife.org) (2007, background): “Among these, the taxon ID tree, which employs varied distance metrics to generate a neighbour-joining (NJ) tree based on nucleotide or amino acid sequences (Saitou & Nei 1987; Howe et al .”
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix (2009, methodology): “Large alignments often contain many sequences that are exactly identical to each other (Howe et al. 2002).”
Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote (2006, neutral): “] and bootstrapped neighbor-joining trees are produced using QuickTree [”