Insertions and deletions constitute the second most important source of natural genomic
variation. Insertions and deletions make up to 25% of genomic variants in humans and are …

Insertions and deletions (indels) are common molecular evolutionary events. However,
probabilistic models for indel evolution are under-developed due to their computational …

Motivation Insertions and deletions (indels) of short DNA segments, along with substitutions,
are the most frequent molecular evolutionary events. Indels were shown to affect numerous …

The classic methodology of inferring a phylogenetic tree from sequence data is composed of
two steps. First, a multiple sequence alignment (MSA) is computed. Then, a tree is …

Perfect short inverted repeats (IRs) are known to be enriched in a variety of bacterial and
eukaryotic genomes. Currently, it is unclear whether perfect IRs are conserved over …

The evaluation of phylogenetic inference tools is commonly conducted on simulated and
empirical sequence data alignments. An open question is how representative these …

A large body of research is dedicated to model sequence evolutionary dynamics. The
evolutionary process may vary within groups of genes, among sites within a gene, between …

Classic alignment algorithms utilize scoring functions which maximize similarity or minimize
edit distances. These scoring functions account for both insertion–deletion (indel) and …

Disentangling evolutionary signal from noise in genomic datasets is essential to building
phylogenies. The efficiency of current sequencing platforms and workflows has resulted in a …

Accurately reconstructing pairwise sequence alignments (PWAs) and/or multiple sequence
alignments (MSAs) is a central step in the study of homologous (ie, ancestor-sharing) …