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Basam Al Nashéa: Algorithm for Perfect Phylogeny and Gene Reconciliation

Master thesis

Time: Thu 2023-02-09 11.00 - 12.00

Location: Cramer Room , Albano

Respondent: Basam Al Nashéa

Supervisor: Lars Arvestad

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A Perfect Phylogeny TG for a set of genes G describes their com- mon evolutionary lineage under the constraint that no two properties have evolved in separate places within that lineage. The problem of Reconciliation, under one particular model, is that of mapping the evo- lutionary tree TG to a species tree S of the species that harbor the genes in G, with the goal of annotating the internal vertices with duplication or speciation. The biological significance is that this provides insight into which gene sequences are paralogous and orthologous. We develop a combined algorithm for excecuting both tasks based on merging two existing algorithm for each separate task of finding a perfect phylogeny, and then reconciling it.