The study of Genomes of organisms

https://www.wikiwand.com/en/Genomics

https://genome-euro.ucsc.edu/cgi-bin/hgGateway?hgsid=218799371_GrzgaLCTgLS4ixN0o64W7m83y2na

Comparative genomics

Has uses in Biochemical genetics, Population genetics, etc..

Bioinformatics

Haplotype inference – Infering the Haplotypes (the two homologous chromosomes) from genomic data.

DNA sequencing just gives all the base pairs at each position, but doesn't give which belong together in a single chromosome/haplotype.

Heterozygous SNPs are the ones which are non-trivial to assign to the chromosome/haplotype.

• Clark's algorithm: a parsimony approach. Try to minimize the different number of haplotypes,
• Statistical model approach. Find all potential haplotypes consistent with data. Model assigns a population frequency to each haplotype. If we know these frequencies we can assign the most probable haplotypes to each individual. Missing data problem –> EM algorithm
• Bayesian methods. Allow haploids which are different, but similar to influence each other's likelihood. Hidden Markov model.