Jūlija Pečerska

The paper evaluates ARPIP's ability to reconstruct ancestral sequences with long indels, showing it preserves gap length distributions and captures deletion bias in mammalian proteins.

This paper introduces indelMaP, a method that improves ancestral sequence reconstruction and multiple sequence alignment by treating insertions and deletions as distinct evolutionary events, achieving high accuracy and speed for densely sampled datasets.

This paper introduces a combinatorial optimization method to jointly infer multiple sequence alignments and phylogenetic trees under maximum likelihood, addressing computational limitations of existing approaches.