The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
PyCogent: a toolkit for making sense from sequence
Open accessAbstract
We have implemented in Python the COmparative GENomic Toolkit, a fully integrated and thoroughly tested framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics. PyCogent includes connectors to remote databases, built-in generalized probabilistic techniques for working with biological sequences, and controllers for third-party applications. The toolkit takes advantage of parallel architectures and runs on a range of hardware and operating systems, and is available under the general public license from http://sourceforge.net/projects/pycogent.
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Cites
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Stamatakis, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl446 · Cited by 15,582
<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool
Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480
UniFrac: a New Phylogenetic Method for Comparing Microbial Communities
Lozupone, C., & Knight, R. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.12.8228-8235.2005 · Cited by 8,227
Self-citationPowell, M. J. D. (1964) · The Computer Journal · doi:10.1093/comjnl/7.2.155 · Cited by 4,632 · cited 3×
“The numerical optimization process used here is simulated annealing [37] followed by the Powell algorithm [38].”
MethodA codon-based model of nucleotide substitution for protein-coding DNA sequences.
(1994) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040153 · Cited by 1,960
Global Optimization of Statistical Functions with Simulated Annealing
Goffe, W. L., Ferrier, G. D., & Rogers, J. (1994) · Journal of Econometrics · doi:10.1016/0304-4076(94)90038-8 · Cited by 1,610
DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.
Morgenstern, B. (1999) · Bioinformatics · doi:10.1093/bioinformatics/15.3.211 · Cited by 678
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Self-citationA core gut microbiome in obese and lean twins
Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., et al. (2009) · Nature · doi:10.1038/nature07540 · Cited by 7,823
Self-citationPyNAST: a flexible tool for aligning sequences to a template alignment
Caporaso, J. G., Bittinger, K., Bushman, F. D., DeSantis, T. Z., Andersen, G. L., & Knight, R. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp636 · Cited by 3,396
Self-citationDiet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans
Muegge, B. D., Kuczynski, J., Knights, D., Clemente, J. C., González, A., Fontana, L., Henrissat, B., Knight, R., & Gordon, J. I. (2011) · Science · doi:10.1126/science.1198719 · Cited by 1,988
Self-citationEvolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues
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Metadata
- Authors
- Knight, R., Maxwell, P., Birmingham, A., Carnes, J., Caporaso, J. G., Easton, B. C., Eaton, M., Hamady, M., Lindsay, H., Liu, Z., Lozupone, C., McDonald, D., Robeson, M., Sammut, R., Smit, S., Wakefield, M. J., Widmann, J., Wikman, S., Wilson, S., Ying, H., & Huttley, G. A.
- Venue
- Genome Biology
- Published
- 2007-08-21
- Volume
- 8
- Issue
- 8
- Pages
- R171-R171
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- OpenAlex
- W2143980572
- Cited by
- 195
- References
- 7
- FWCI
- 3.71
- Type
- journal article
- Language
- en
- Open access
- gold
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- CoChat. (2026). Citation check: PyCogent: a toolkit for making sense from sequence. https://app.cochat.ai/papers/10.1186/gb-2007-8-8-r171
- The paper
- Knight, R., Maxwell, P., Birmingham, A., Carnes, J., Caporaso, J. G., Easton, B. C., Eaton, M., Hamady, M., Lindsay, H., Liu, Z., Lozupone, C., McDonald, D., Robeson, M., Sammut, R., Smit, S., Wakefield, M. J., Widmann, J., Wikman, S., Wilson, S., . . . Huttley, G. A. (2007). PyCogent: a toolkit for making sense from sequence. Genome Biology. https://doi.org/10.1186/gb-2007-8-8-r171
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
