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Table 3 Summary of programs to remove chimeras

From: A review of software for analyzing molecular sequences

Chimera program Year published Method Advantage
CHIMERA_CHECK[15] 1999   Initial program
Bellerphon[16] 2004 Partial treeing approach Initial program
Pintail[17] 2005 Reference database comparing variation differences More sensitive than earlier methods
Ccode[19] 2005 Reference of putative chimeras, measuring variability Bypasses need for manual inspection
Mallard[18] 2006 Reference database comparing variation differences to all pairs More sensitive than earlier Pintail program
ChimeraChecker[20] 2010 Focuses on ITS region using BLAST Used for fungal sequences
ChimeraSlayer[12, 21] 2011 Reference database constructs potential alignments with parent strands Useful for short sequences and where parents of chimeras are closely related – more sensitive than earlier methods
Perseus[12, 22] 2011 Searches for parts of parent sequences in higher abundance de novo sequences from 454 pyrosequencing reads
UCHIME[12, 14] 2011 Uses multiple reference databases, aligning to top hits and computes score Faster without sacrificing sensitivity, identifying chimeras with more than two parents
DECIPHER[23] 2012 Search-based approach, detecting short fragments Useful for short sequences