Locityper provides ability to globally align (opens in a new tab) input haplotypes or other small to medium-size sequences. For that, you can use locityper align. Note, that this operation is probably slower than Minimap2 alignment, but, on the other hand, it provides global alignment without splitting the alignment into overlapping primary/secondary/supplementary subalignments.

To align all pairwise sequences, please use

locityper align -i sequences.fasta -o alignments.paf.gz -A

In addition, you can align specific pairs using

locityper align -i sequences.fasta -o alignments.paf.gz \
    -p name1,name2 name3,name4 ...

The same effect can be achieved using -P and a two column file with sequence names. Before v1.7.0 sequences with high minimizer divergence were skipped. You can bring back that behavior using -D argument.

Since v1.7.0 Locityper speeds up alignment construction using transitive alignment transfer (quickly construct alignment A-C using existing alignments A-B and B-C). This transfer is controlled by an argument --tr-div, with smaller values leading to stricter conditions on the previous alignments. You can completely disable alignment transfer using --tr-div 0. This will lead to slightly more accurate alignments at a significant runtime cost.

If transitive alignments are allowed, it may be beneficial to align all pairs (-A) instead of a subset of pairs (-P), since the subset may contain few triangles and therefore be much slower to process.