Alignment quality & statistics

• Alignment entropy - Shannon entropy across alignment sites

• Alignment length - Length of an input alignment

• Alignment length no gaps - Alignment length excluding gapped sites

• Alignment outlier regions - Detect localized outlier regions in multiple sequence alignments

• Alignment outlier taxa - Identify outlier taxa in alignments

• Codon dN/dS - Pairwise synonymous and nonsynonymous substitution-rate estimates

• Column score - Column score for alignment quality

• Composition per taxon - Nucleotide or amino acid composition per taxon

• Compositional bias per site - Detect compositional bias across sites

• Evolutionary Rate per Site - Site-specific evolutionary rate estimation

• Guanine-cytosine (GC) content - GC content of an alignment

• Identity matrix - Pairwise sequence identity heatmap

• Occupancy per taxon - Taxon occupancy in alignment columns

• Pairwise identity - Pairwise sequence identity in an alignment

• Parsimony informative sites - Count parsimony informative sites

• Plot alignment QC - Visual quality control plots for alignments

• Relative composition variability - Composition variability across taxa

• Relative composition variability, taxon - Per-taxon relative composition variability

• Sum-of-pairs score - Sum-of-pairs alignment quality score

• Variable sites - Count variable sites in an alignment