0 user reviews
0 user reviews
Already have an account? Sign in to review this tool.
No review has been posted.
No open topic.
- Software type:
- Restrictions to use:
- Programming languages:
- Command line interface
- Operating system:
- Unix/Linux, Mac OS, Windows
- Computer skills:
- Python, Argparse Numpy, Scipy libraries
(Silvestro et al., 2014) Bayesian estimation of speciation and extinction from incomplete fossil occurrence data. Systematic Biology.
(Silvestro et al., 2014) PyRate: A new program to estimate speciation and extinction rates from incomplete fossil record. Methods in Ecology and Evolution.
- Documentation: https://github.com/dsilvestro/PyRate/wiki
- Daniele Silvestro <daniele.silvestro at unil.ch>
Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland; Department of Plant and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden; Biodiversity and Climate Research Centre & Senckenberg Research Institute, Frankfurt am Main, Germany; Department of Biological Sciences, Goethe University, Frankfurt am Main, Germany; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway; Gothenburg Botanical Garden, Gothenburg, Sweden
This project was funded from the German Academic Exchange Service, the University of Lausanne, the Wenner-Gren Foundation, the LOEWE program of Hesse’s Ministry of Higher Education Research and the Arts, the Swedish Research Council (B0569601), the European Research Council under the European Unions Seventh Framework Programme (FP/2007-2013, ERC Grant Agreement No. 331024), the grants PDFMP3_134931 and 3100A0_138282 from the Swiss National Science Foundation.
Link to literature
Review of tools
Related Phylogenetic inference tools
Supports multiple kinds of data (e.g. morphology, nucleotides, genes and gene…
Supports multiple kinds of data (e.g. morphology, nucleotides, genes and gene regions, chromosomes, whole genomes, etc). POY is a phylogenetic analysis program that can perform true sequence…
Provides distance algorithms to infer phylogenies. FastME is based on balanced…
Provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of Neighbor Joining (NJ). FastME improves over NJ by performing…
Supports dynamic browsing of motif trees with custom collapse/expansion of…
Supports dynamic browsing of motif trees with custom collapse/expansion of branches. RSAT matrix-clustering also provides multiple ways to inspect the results: motif forest with branch motifs at each…
Can harness the idle computing resources of any research institute to construct…
Can harness the idle computing resources of any research institute to construct large phylogenetic trees using maximum likelihood. DPRml uses an already proven maximum likelihood-based tree building…
Allows the complete Ensembl gene database to be queried using phylogenetic…
Allows the complete Ensembl gene database to be queried using phylogenetic patterns. PhyloPat offers the possibility of querying with binary phylogenetic patterns or regular expressions, or through a…