Aligning short reads to reference alignments and trees

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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability (2013, methodology): “Several tools (Berger and Stamatakis 2011; Löytynoja et al. 2012; Sun and Buhler 2012) for this purpose were developed between 2011 and 2012.”
PhyLAT: a phylogenetic local alignment tool (2012, methodology): “PaPaRa (Berger and Stamatakis, 2011), unlike the tools described above, uses a guide tree to map queries, in particular short reads, to an existing multiple alignment, but it does not score or improve the resulting alignments probabilistically given the phylogeny.”
Computational meta'omics for microbial community studies (2013, methodology): “(MEGAN (Huson et al, 2007)) or other parsimonious evolutionary principles (PaPaRa (Berger and Stamatakis, 2011)).”
EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences (2018, methodology): “It effectively strips the input Multiple Sequence Alignments (MSAs) of all sites that are unlikely to contribute substantially to the placement likelihood score.”
Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm (2012, methodology): “The methods tested for both were PAGAN/guided, PAGAN/free (v.0.33), hmmalign (from the HMMER package, v.3.0; Eddy, 2011), MAFFT (v.6.860b; Katoh et al., 2002) and ClustalW (v.2.1; Larkin et al., 2007); for DNA we also used PaPaRa (RAxML v.7.2.6; Berger and 1687 [16:07 19/6/2012 Bioinformatics-bts198”