Sharif Digital Repository

Human is diploid specie that inherits a set of chromosomes from their mother and a set from their father. The process of separating the nucleotide content of a set of extracted maternal and paternal chromosomes for an individual or a population is called phasing the genome of the individual or the population. The placement of any two variants relative to each other in diploid species is possible in two forms: cis (placement of both variants on one chromosome), and trans (placement of variants on different chromosomes). Each of these conditions leads to different phenotypes. Thus, understanding how variants are placed relative to each other is a crucial problem in human biology which is... 

One of the branches of genetic studies is population genetics. Each population has its own characteristics due to its evolutionary history, cultural characteristics and geography, which distinguish it from other populations. Scientific and technological advances in recent decades have led to the production of new generation sequencing machines and the creation of large genetic data. These data contain important genetic information and answers to many questions about the origin of humans, the history of populations and their evolutionary process. More and better understanding of the human genome and the distance between populations can help to better understand biological mechanisms and deal... 

One of the cornerstones of population genetics is finding ancestral relations between people of a population. Mutations and recombinations are two major signals that can be exploited to infer the population ancestral relationships. Next Generation Sequencing (NGS) has paved the way for achieving this endeavor by providing massive data including single nucleotide polymorphisms, insertions, and deletions as well as structural variations between individuals. In this thesis, the goal is to infer the ancestral structure of a given gene from thousands of NGS datasets. We also attempt to decode times of important events including mutations and recombinations. To this end, we first split a gene into...