Fig. 11
From: Split-alignment of genomes finds orthologies more accurately
Probabilistic models for segments and local alignments. a Segment model. b Segment set model. c Alignment model. States labeled B (background) emit letter x with probability θ x . States labeled F (foreground) emit letter x with probability π x . The state labeled M (match) emits aligned letters x:y with probability π xy . States labeled D (delete) emit reference letters x with probability ϕ x . States labeled I (insert) emit query letters y with probability ψ y . Small circles are just connectors and do not emit