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PyCogent specifications


Unique identifier OMICS_14006
Name PyCogent
Alternative names PYthon Comparative GENomic Toolkit, Cogent
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.9
Stability Stable
Numpy, zlib, C compiler, Matploblib, Cython, mpi4py, SQLAlchemy
Maintained No




No version available



This tool is not available anymore.

Publication for PYthon Comparative GENomic Toolkit

PyCogent citations


Mining for recurrent long range interactions in RNA structures reveals embedded hierarchies in network families

Nucleic Acids Res
PMCID: 5934684
PMID: 29608773
DOI: 10.1093/nar/gky197
call_split See protocol

[…] lows. First all canonical Watson–Crick and wobble base pairs (i.e. A-U, G-C and G-U) were identified. Then, since many structures are naturally pseudoknotted, we used the K2N () implementation in the PyCogent () Python module to remove pseudoknots. Problems arise when a nucleotide is involved in several Watson–Crick base pairs (which is geometrically not feasible), probably due to an error of the […]


Influenza A virus infection impacts systemic microbiota dynamics and causes quantitative enteric dysbiosis

PMCID: 5763955
PMID: 29321057
DOI: 10.1186/s40168-017-0386-z

[…] ples (β-diversity) and relative abundance of bacterial communities were calculated using standard QIIME workflow ( with sampling depth of 200, 400, 20,000 OTUs, chosen by a PyCogent algorithm, for the lung, the small intestine, and fecal samples, respectively. Chao1 estimator [, ] and Shannon H-index [] were used to evaluate community richness through alpha diversity (Ad […]


Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (Sus scrofa)

Ecol Evol
PMCID: 5756863
PMID: 29321862
DOI: 10.1002/ece3.3638

[…] (Edgar, ) (Edgar, ) was used to create reference databases that correspond to the specific amplicon regions of the trnL and CO1 marker sequences from all downloaded GenBank (Benson et al., ) records. PyCogent (Knight et al., ) was used to extract the full taxonomic lineage using the gi‐to‐taxid mapping files provided by GenBank. All extracted amplicon regions were dereplicated to 100% sequence ide […]


Crystal structure and RNA binding properties of an Hfq homolog from the deep branching Aquificae: conservation of the lateral RNA binding mode

Acta Crystallogr D Struct Biol
PMCID: 5379935
PMID: 28375142
DOI: 10.1107/S2059798317000031

[…] (iii) the ‘reduced surface’ analytical approach of MSMS (Sanner et al., 1996), and the more approximate (point-counting) methods from the structural analysis routines available in (iv) PyMOL and (v) PyCogent (Cieślik et al., 2011).All molecular-graphics illustrations in Figs. 5–8 and Supplementary Figs. S3–S6 were created in PyMOL, with the exception of Supplementary Figs. S4(e) and S4(f) (create […]


A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits

Mol Biol Evol
PMCID: 5435079
PMID: 28369572
DOI: 10.1093/molbev/msx055
call_split See protocol

[…] en rerooting Newick trees. After reporting the issue, a previously undocumented option (–s) has been documented that permits to automatically interpret inner node labels as branch support attributes. Pycogent interprets inner node labels as support values by default and those are correctly handled by the rooting functions. […]


Diversity and enterotype in gut bacterial community of adults in Taiwan

BMC Genomics
PMCID: 5310273
PMID: 28198673
DOI: 10.1186/s12864-016-3261-6

[…] to the OTU table. There are three steps in deciphering the enterotype of stool samples []. The first step is to calculate the distance matrix of β-diversity. R package “vegan” [] and Python software “Pycogent” [] were employed to calculate nine types of matrices, namely Alternative Gower, Bray Cutris, Jaccard, Kulczynski, Chebyshev, Pearson, Horn, Euclidean, and Weighted UniFrac. The second step i […]


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PyCogent institution(s)
Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO, USA; Computational Genomics Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, Australia; Thermo Fisher Scientific, Lafayette, CO, USA; Seattle Biomedical Research Institute, Seattle, WA, USA; Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Aurora, CO, USA; Science Applications International Corporation, Englewood, CO, USA; Department of Computer Science, University of Colorado, Boulder, CO, USA; Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA; Walter and Eliza Hall Institute, Melbourne, Australia
PyCogent funding source(s)
This tool was funded by the Australian Partnership for Advanced Computing, Cray Australia Pty. Ltd., the Australian Research Council, the National Health and Medical Research Council, the Keck RNA Bioinformatics Initiative, Jane and Charlie Butcher Foundation, NIH Signaling and Cellular Regulation Training Grant, NIH Biophysics Training Grant, the National Academy Keck Futures Initiative

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