An open source chimera checker for the fungal ITS region
Version of Record online: 14 MAR 2010
© 2010 Blackwell Publishing Ltd
Molecular Ecology Resources
Volume 10, Issue 6, pages 1076–1081, November 2010
How to Cite
NILSSON, R. H., ABARENKOV, K., VELDRE, V., NYLINDER, S., DE WIT, P., BROSCHÉ, S., ALFREDSSON, J. F., RYBERG, M. and KRISTIANSSON, E. (2010), An open source chimera checker for the fungal ITS region. Molecular Ecology Resources, 10: 1076–1081. doi: 10.1111/j.1755-0998.2010.02850.x
- Issue online: 14 MAR 2010
- Version of Record online: 14 MAR 2010
- Received 1 September 2009; revision received 4 February 2010; accepted 10 February 2010
Data S1 The software package together with its documentation, reference sequences from INSD and a test data set (including, for illustratory purposes, 10 sequences that are clearly chimeric, 10 sequences that are clearly nonchimeric and 10 sequences that cannot be processed for the lack of enough sequence data). In addition, the user will have to install ncbi-blast, hmmer, and one of Clustal W, mafft, and dialign-tx; detailed installation instructions are provided in the documentation. The underlying directory was archived with tar and compressed with zip.
Data S2 A screenshot of the software package in operation on a dual core MacBook Pro running OS X 10.4.11.
Data S3 Hidden Markov models for the nuclear large and small subunits and the 5.8S for animals and oomycetes (Oomycota), provided to facilitate the implementation of the software for other organism groups where ITS sequences are used for scientific purposes. The models are based on inclusive alignments designed to capture the full width of the lineages. As with fungi, however, some taxa can be expected to have sequences deviant enough as to preclude automated attempts at locating the ITS1 and ITS2 with kingdom-level HMMs (cf. Feibelman et al. 1994).
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