The Cumulative Indel Model: fast and accurate statistical evolutionary alignment

Sequence alignment is essential for phylogenetic and molecular evolution inference, as well as in many other areas of bioinformatics and evolutionary biology.
Inaccurate alignments can lead to severe biases in most downstream statistical analyses.
Statistical alignment based on probabilistic models of sequence evolution addresses these issues by replacing heuristic score functions with evolutionary model-based probabilities.
However, score-based aligners and fixed-alignment phylogenetic approaches are still more prevalent than methods based on evolutionary indel models, mostly due to computational convenience.
Here, I present new techniques for improving the accuracy and speed of statistical evolutionary alignment.
The \"cumulative indel model\" approximates realistic evolutionary indel dynamics using differential equations.
\"Adaptive banding\" reduces the computational demand of most alignment algorithms without requiring prior knowledge of divergence levels or pseudo-optimal alignments.
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