Domainhound

Domainhound leverages hmmer3 to assign domains to protein sequences. Takes multiple protein fasta files which may contain entire gene sets from species, and hidden-Markov models from Pfam or generated by the user. Provides results for each sequence with domain information in text format convenient for further analysis. Provides a phylogenetic table showing the number of occurrences of domain hits in input species. Identifies the highest scoring domain in case of overlaps. Useful for classifying protein sequences based on domain content with high throughput.