Alignment & dataset utilities

• Alignment recoding - Recode alignment into reduced alphabets

• Alignment subsampling - Randomly subsample genes, partitions, or sites

• Create concatenation matrix - Concatenate multiple alignments into a supermatrix

• Faidx - Extract entries from FASTA files

• Mask alignment - Mask sites in an alignment

• Occupancy filter - Filter alignments or trees by cross-file taxon occupancy (works with both FASTA and Newick)

• Protein-to-nucleotide alignment - Thread nucleotide onto protein alignment

• Rename FASTA entries - Rename entries in a FASTA file

• Taxon groups - Group alignment or tree files by shared taxon sets (works with both FASTA and Newick)