The method presented in this article extends the GHMMs used in single isoform gene finding [24] to explicitly model features of alternative and constitutive exons. The features of the explicit alternative splicing prediction methods: k-mer counts, exon lengths, and sequence conservation are used to predict multiple splice sites and intron retention events along with cassette exons and constitutive exons. Cross-species sequence conservation is incorporated using components of the single isoform phylogenetic HMM gene finders [25-27]. The phylogenetic shadowing principle is used to assume a multiple sequence alignment can be obtained from closely related species [28]. In contrast, the pair-HMM method simultaneously predicts a pairwise alignment and the exon structure making it potentially better suited to incorporate a difficult to align, more distantly related organism. Conservation from greater evolutionary distances may improve discriminative power in identify functional nucleotides, but with the potential trade off of detecting a smaller set of conserved alternative splicing events [29].