ArticleBMC bioinformatics2009
PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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40 citing papers in PubMed.
- Effect of a Probiotic Beverage Enriched with Cricket Proteins on the Gut Microbiota: Composition of Gut and Correlation with Nutritional Parameters.Foods (Basel, Switzerland) · 2024Article
- Methods to Identify and Study the Evolution of Pseudogenes Using a Phylogenetic Approach.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Genome sequence and description ofNew microbes and new infections · 2019Article
- Non-contiguous finished genome sequencing and description ofNew microbes and new infections · 2019Article
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- Noncontiguous finished genome sequences and description ofNew microbes and new infections · 2018Article
- Genome analysis and description ofNew microbes and new infections · 2018Article
- Eggerthella timonensis sp. nov, a new species isolated from the stool sample of a pygmy female.MicrobiologyOpen · 2018Article
- Genomic and phenotypic description of the newly isolated human species Collinsella bouchesdurhonensis sp. nov.MicrobiologyOpen · 2018Article
- Noncontiguous finished genome sequences and descriptions ofNew microbes and new infections · 2018Article
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- Taxonogenomic description of four newNew microbes and new infections · 2018Article
- Noncontiguous finished genome sequences and descriptions ofNew microbes and new infections · 2017Article
- Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life.Genes · 2017Article
- Noncontiguous finished genome sequences and description ofNew microbes and new infections · 2017Article
- Hugonella massiliensis gen. nov., sp. nov., genome sequence, and description of a new strictly anaerobic bacterium isolated from the human gut.MicrobiologyOpen · 2017Article
- Genome sequence and description ofNew microbes and new infections · 2017Article
- Identification of constraints influencing the bacterial genomes evolution in the PVC super-phylum.BMC evolutionary biology · 2017Article
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Authors and funding
3 authors.
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Abstract
backgroundTo effectively apply evolutionary concepts in genome-scale studies, large numbers of phylogenetic trees have to be automatically analysed, at a level approaching human expertise. Complex architectures must be recognized within the trees, so that associated information can be extracted.
resultsHere, we present a new software library, PhyloPattern, for automating tree manipulations and analysis. PhyloPattern includes three main modules, which address essential tasks in high-throughput phylogenetic tree analysis: node annotation, pattern matching, and tree comparison. PhyloPattern thus allows the programmer to focus on: i) the use of predefined or user defined annotation functions to perform immediate or deferred evaluation of node properties, ii) the search for user-defined patterns in large phylogenetic trees, iii) the pairwise comparison of trees by dynamically generating patterns from one tree and applying them to the other.
conclusionPhyloPattern greatly simplifies and accelerates the work of the computer scientist in the evolutionary biology field. The library has been used to automatically identify phylogenetic evidence for domain shuffling or gene loss events in the evolutionary histories of protein sequences. However any workflow that relies on phylogenetic tree analysis, could be automated with PhyloPattern.
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