In brief, performance assessment and comparison of multiple trimming alignment software revealed that ClipKIT is a top-performing software.
ClipKIT is a top-performing software for trimming multiple sequence alignments. Across a total of 138,152 multiple sequence alignments (MSAs) from empirical (left) and simulated (right) datasets, desirability-based integration of accuracy and support metrics per MSA facilitated the comparison of relative software performance and revealed ClipKIT is a top-performing software. MSA trimming approaches are ordered along the x-axis from the highest-performing software (left) to the lowest-performing software (right) according to average desirability-based rank, which is derived from measures of tree accuracy (i.e., normalized Robinson Foulds distance) and tree support (i.e., average bipartition support).
Abbreviations of trimmers and parameters are as follows: ClipKIT: g = gappy mode; ClipKIT: kc = kpic; ClipKIT: kcg = kpic-gappy; ClipKIT: k = kpi mode; ClipKIT: kg = kpi-gappy mode; BMGE = BMGE default; BMGE 0.3 = 0.3 entropy threshold; BMGE 0.7 = 0.7 entropy threshold; trimAl: s = strict; trimAl: sp = strictplus; Noisy = default; Gblocks = default; No trim = no trimming.
For additional details about performance assessment, please see ClipKIT: a multiple sequence alignment trimming software for accurate phylogenomic inference. Steenwyk et al. PLoS Biology. doi: 10.1371/journal.pbio.3001007.