PrepareAlign deletes gap-rich sequences from the alignment
Parent program: augustus
AUGUSTUS is a software to predict genes in eukaryotic genomic sequences.The approach is based on a generalized Hidden Markov Model. AUGUSTUS parses a genomic sequence to segments that are most likely according to the underlying statistical models. The program is often the most accurate for ab initio gene prediction for the species it is trained for. AUGUSTUS is able to incorporate EST, mRNA and protein alignments. It also can predict alternative transcripts, splicing and 5'UTR and 3'UTR including introns with probabilities for the transcripts and each exon and intron.