Please find shell wrappers for some of the EMBOSS utilities to make them compatable with metagenomic whole-genome shotgun contigs:

• compseq.sh: calculate the composition of unique words in sequences
• dan.sh: calculate nucleic acid melting temperature
• density.sh: calculate nucleic acid density
• cpgreport.sh: identify and report CpG-rich regions in nucleotide sequence
• newcpgreport.sh: identify CpG islands in nucleotide sequence
• fuzznuc.sh: search for patterns in nucleotide sequences
• fuzztran.sh: search for patterns in protein sequences (translated)
• freak.sh: generate residue/base frequency table
• etandem.sh: find tandem repeats in a nucleotide sequence
• tcode.sh: identify protein-coding regions using Fickett TESTCODE statistic
• getorf.sh: find and extract open reading frames (ORFs)

Best Wishes,
Umer