Table 1.
The 14 different MSA trimming strategies tested in this study.
Fig 1.
The 14 alignment trimming strategies tested differ in resulting MSAs and metrics of phylogenetic tree accuracy and support.
Principal component analysis of alignment length, nRF, and ABS values across the 14 MSA trimming strategies for 4 empirical datasets (A) and 4 simulated datasets (B). Insets of scree plots depict the percentage of variation explained (y-axis) for the first 5 dimensions (x-axis). Data were scaled prior to conducting principal component analysis. Note that the BMGE 0.3 and Gblocks strategies are not represented in Fig 1B because they frequently removed entire alignments and were therefore removed from the analysis of simulated sequenced. Data used to generate this figure can be found on figshare (doi: 10.6084/m9.figshare.12401618). ABS, average bipartition support; BMGE, Block Mapping and Gathering with Entropy; MSA, multiple sequence alignment; nRF, normalized Robinson–Foulds.
Fig 2.
ClipKIT is a top-performing software for trimming MSAs.
Desirability-based integration of accuracy and support metrics per MSA facilitated the comparison of relative performance of the 14 different MSA trimming strategies for empirical (A–D) and simulated (E–H) datasets. Examination of performance for individual datasets and average performance across empirical (I) and simulated (J) datasets revealed that ClipKIT is a top-performing software. MSA trimming strategies are ordered along the x-axis from the highest-performing strategy to the lowest-performing one according to average desirability–based rank. Boxplots embedded in violin plots have upper, middle, and lower hinges that represent the first, second, and third quartiles. Whiskers extend to 1.5 times the interquartile range. Data used to generate this figure can be found on figshare (doi: 10.6084/m9.figshare.12401618). AA, amino acid; BMGE, Block Mapping and Gathering with Entropy; MSA, multiple sequence alignment; NT, nucleotide.