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 | Â | 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 |
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 | |
2011 | Searches for parts of parent sequences in higher abundance | de novo sequences from 454 pyrosequencing reads | |
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 |