BPS 4104 Lecture Notes - Lecture 8: Homeobox, Operational Definition, Forkhead Box L2
27 Mar 2018
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Will see 2 bands bc insertion of u at posn 79 in thalass. Illustrations of poor alignment (in red) in the sequence data from the supplementary file (nature08742-s2. nex) in regier et al. (2010) for a subset of six species (a), with the shared gaps deleted. The proper alignment of the red-colored sequences is shown in (b). The top alignment was said to be aligned by mafft. Homology: similarity that is the result of inheritance from a common ancestor (identification and analysis of homologies is central to phylogenetic systematics). An alignment is an hypothesis of positional homology between bases/amino acids. The fundamental assumptions: shared ancestry that is computationally identifiable. The criterion: maximum alignment score given a scoring scheme. The two words share ancestry, with one being evolved from the other or both from a common ancestor. If favorite is ancestral, then an insertion event of u between sites 4 and 5 has happened during the evolution of the word.
