The Chimera Detection program accepts a sequence file and returns a histogram that may indicate whether your sequence(s) is of chimeric origin. A detailed description of how the analysis procedure is available.

Users with multiple environmental sequences might also want to try the Bellerophon chimera detection program by Phil Hugenholtz and Thomas Huber.

New in 2005 -- Pintail is a tool for identifying anomalies such as chimeras within 16S rDNA sequences. The program works by comparing evolutionary distances between a query and subject sequence over the length of the 16S rRNA gene (small subunit rRNA), by employing a sampling window of specified size, progressing a fixed number of bases at a time along the length of the gene. It is released under the terms of the GNU General Public Licence and is freely available from the people who brought you Primrose.