Ancestral sequence reconstruction is an established bioinformatic method for inferring the likely character states of the ancestors of a set of modern day biological sequences. Ancestral proteins are studied because they provide insight into how modern proteins have evolved and how they are able to perform their specific functions. Ancestors are also routinely used as starting points for protein engineering due to the identification of critical residues for targeted mutagenesis and the viability of ancestral templates for further engineering. Existing tools for performing ancestral sequence reconstruction are currently unable to process more than several hundred modern day sequences at a time meaning there is a vast amount of information that is missing from current analyses. This thesis extends the field of ancestral research by 1) introducing a novel reconstruction tool, Graphical Representation of Ancestral Sequence Predictions (GRASP), which is capable of inferring the ancestors of data sets of previously unattainable sizes, 2) developing workflows for data sets that contain multiple protein subunits, and 3) providing tools and metrics for automating and evaluating reconstruction. Biological sequences evolve by single site mutational events as well as insertion or deletion of biological content. Increasing the size of data sets naturally increases the number of evolutionary events that must be modelled and processed. GRASP handles this increased complexity by employing partial order graphs, a graphical model that allows for alternative evolutionary histories due to insertion and deletion of content to be evaluated and explored. GRASP is validated across multiple protein families via the successful inference and synthesis of biological ancestors that are now able to be constructed from substantially larger data set sizes. Modelling ancestors as partial order graphs also enables a novel form of protein engineering capable of re-purposing the insertions and deletions used throughout evolutionary time in order to design novel proteins with insertion and deletion of content inspired from, but not directly present in, their shared ancestral sequences. This thesis shows, via a reconstruction of four modified cytochrome P450 subfamily 2U1 ancestors, that this novel engineering method is a viable technique capable of producing meaningful ancestors with altered properties.