anno tool module anno.tl

Alignment

motif_msa	Align motif sequences using progressive MSA or pairwise reference alignment.
sample_msa	Multiple sequence alignment of motif arrays across samples.

Motif Abundance

motif_abundance_pca

PCA on motif abundance percentage vectors.

Haplotype Calling

haplotype_neighbor	Build a fused kNN graph from aligned motif arrays for haplotype analysis.
haplotype_leiden	Cluster samples into haplotypes using Leiden on the fused graph.
haplotype_leiden_res_scan	Scan Leiden resolution and record cluster counts + modularity.