TEclass classifies unknown transpsosable element (TE) consensus sequences into four categories, according to their mechanism of transposition: DNA transposons, LTRs, LINEs, SINEs.
ConsensusFixer is a java command line application which computes a consensus sequence with in-frame insertions and ambiguous nucleotide (wobbles) from ultra deep next-generation sequencing alignments.
Refcomp was designed to analyze sequencing traces which contains data from strictly homozygous samples (eg. cloned DNA, mitochondrial DNA, etc.). This data represents a special case which can be analyzed for mismatches with a known reference sequence. Refcomp will determine the high quality positions within an assembled DNA contig and produce a report listing sites which differ from a defined reference sequence.
Refcomp is designed as a member of an integrated suite of sequence analysis applications which includes Phred,Phrap and Consed, and is not a stand alone program.
RefComp is available for free to researchers at academic and non-profit institutions. To aquire RefComp, please Read the Academic License Agreement, and fill in and submit the request form.