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PTP | A general species delimitation method with applications to phylogenetic placements

A model for delimiting species on a rooted phylogenetic tree. PTP model speciations or branching events in terms of number of substitutions. So it only requires a phylogenetic input tree, for example the output of RAxML. It can easily be integrated with the EPA (evolutionary placement algorithm) to calculate the number of species in a set of query sequences that have been placed into a specific branch of the reference phylogeny. We implemented an open reference species delimitation pipeline by integrating PTP with the EPA to identify known and new species.

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PTP forum

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PTP classification

PTP specifications

Unique identifier:
OMICS_01526
Software type:
Package/Module
Restrictions to use:
None
Input format:
Newick, NEXUS
Output format:
txt, png, svg, pdf
Programming languages:
Python
Computer skills:
Advanced
Requirements:
Python-setuptools, Python-numpy, Python-qt, Python-scipy, Python-mysqldb, Python-lxml, Python-matplotlib, ÉTÉ
Name:
Poisson Tree Processes
Interface:
Command line interface
Input data:
Phylogenetic trees
Output data:
Bootstrap delimitations, Posterial Log likelihood trace file, Bootstrap values of delimited species, Tree plot
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU Affero General Public License version 3
Stability:
Stable
Maintained:
Yes

PTP distribution

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PTP classification

PTP specifications

Unique identifier:
OMICS_01526
Interface:
Application programming interface
Input data:
Only one phylogenetic tree as input
Output data:
Species delimitation results
License:
GNU General Public License version 3.0
Stability:
Stable
Name:
Poisson Tree Processes
Restrictions to use:
None
Input format:
Newick, NEXUS
Programming languages:
Python
Computer skills:
Advanced
Maintained:
Yes

PTP distribution

download

PTP support

Documentation

Maintainer

  • Alexandros Stamatakis <>
  • Alexandros Stamatakis <>

Credits

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Publications

Institution(s)

The Exelixis Lab, Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Graduate School for Computing in Medicine and Life Sciences, University of Lübeck, Lübeck, Germany; Institut für Neuro- und Bioinformatik, University of Lübeck, Lübeck, Germany; Natural History Museum of Crete, University of Crete, Irakleio, Crete, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas-FORTH, Heraklion, Crete, Greece

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