Phylogeny-aware alignment with PRANK.

By Ari Löytynoja. Methods in molecular biology, 2014

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Using evolutionary data to make sense of macromolecules with a “face‐lifted” ConSurf (2023, background): “…all of its dependencies, (3) at least one of the applications used for multiple sequence alignment (ClustalW [Thompson et al. 1994], PRANK [Löytynoja 2014], MAFFT [Katoh & Standley 2013], or MUSCLE [Edgar 2004]), (4) an application for homolog search (HMMER or the legacy version of…”
Using PhyloSuite for molecular phylogeny and tree‐based analyses (2023, methodology): “For example, for sequence alignment, there are MAFFT [4], MUSCLE [5], PRANK [6], and etc.; for phylogenetic tree reconstruction, commonly used programs are IQ ‐ TREE [7], RAxML [8, 9], MrBayes [10], etc. Finally, these programs often use very different input and output file formats.”
SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments (2016, methodology): “This alignment may have been generated by overlaying SNPs on a consensus reference genome, or using a multiple alignment tool, such as MUSCLE (Edgar, 2004), PRANK (Löytynoja, 2014), MAFFT (Katoh & Standley, 2013), or ClustalW (Thompson et al., 2002).”