ArticleGenome biology2007
PyCogent: a toolkit for making sense from sequence.
Article in Genome biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 123 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
123 citing papers in PubMed.
- evo3D R package: a spatial haplotype framework for structure-informed analysis of molecular evolution.Molecular biology and evolution · 2026Article
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- Stochastic Character Mapping: An Under-Exploited Approach to the Study of Molecular Evolution.Journal of molecular evolution · 2025Article
- A divide-and-conquer approach based on deep learning for long RNA secondary structure prediction: Focus on pseudoknots identification.PloS one · 2025Article
- An explainable machine learning pipeline for prediction of antimicrobial resistance inBioinformatics advances · 2025Article
- Characterizing the diversity and commensal origins ofMicrobial genomics · 2024Article
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- Spectral cluster supertree: fast and statistically robust merging of rooted phylogenetic trees.Frontiers in molecular biosciences · 2024Article
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- Finding recurrent RNA structural networks with fast maximal common subgraphs of edge-colored graphs.PLoS computational biology · 2021Article
- Community Organization and Metagenomics of Bacterial Assemblages Across Local Scale pH Gradients in Northern Forest Soils.Microbial ecology · 2021Article
- EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets.mSystems · 2021Article
- A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics.NAR genomics and bioinformatics · 2020Article
- Machine Learning Techniques for Classifying the Mutagenic Origins of Point Mutations.Genetics · 2020Article
- Advances in monitoring soil microbial community dynamic and function.Journal of applied genetics · 2020Review
- Poultry processing and the application of microbiome mapping.Poultry science · 2020Review
- The Prevalence and Impact of Model Violations in Phylogenetic Analysis.Genome biology and evolution · 2019Article
- Comparative Characterization of Bacterial Communities in Moss-Covered and Unvegetated Volcanic Deposits of Mount Merapi, Indonesia.Microbes and environments · 2019Article
63 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
21 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.