Developing and applying heterogeneous phylogenetic models with XRate

TL;DR

This paper introduces new features in XRate that enable rapid development and prototyping of complex, heterogeneous phylogenetic models, improving efficiency and flexibility in modeling sequence evolution.

Contribution

The paper presents built-in macros and Scheme extensions in XRate for easier implementation of sophisticated phylogenetic models, including lineage-specific and ancestral reconstruction models.

Findings

Enhanced model-prototyping capabilities with macros and Scheme

Improved annotation and lineage-specific modeling features

Demonstrated efficiency in developing complex phylogenetic models

Abstract

Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded gene features. However, beyond a modest level of model complexity, manual coding of models becomes prohibitively labor-intensive. We demonstrate, via a set of case studies, the new built-in model-prototyping capabilities of XRate (macros and Scheme extensions). These features allow rapid implementation of phylogenetic models which would have previously been far more labor-intensive. XRate's new capabilities for lineage-specific models, ancestral sequence reconstruction, and improved annotation output are also discussed. XRate's flexible model-specification capabilities and computational efficiency make it well-suited to developing and prototyping phylogenetic grammar models. XRate is available as part of the DART software package: http://biowiki.org/DART .