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PTP specifications

Information


Unique identifier OMICS_01526
Name PTP
Alternative name Poisson Tree Processes
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Phylogenetic trees
Input format Newick, NEXUS
Output data Bootstrap delimitations, Posterial Log likelihood trace file, Bootstrap values of delimited species, Tree plot
Output format txt, png, svg, pdf
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License GNU Affero General Public License version 3
Computer skills Advanced
Stability No
Requirements
Python-setuptools, Python-numpy, Python-qt, Python-scipy, Python-mysqldb, Python-lxml, Python-matplotlib, ÉTÉ
Maintained No

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Information


Unique identifier OMICS_01526
Name PTP
Alternative name Poisson Tree Processes
Interface Application programming interface
Restrictions to use None
Input data Only one phylogenetic tree as input
Input format Newick, NEXUS
Output data Species delimitation results
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Stability No
Maintained No

Download


Documentation


Maintainer


This tool is not available anymore.

Publication for Poisson Tree Processes

PTP in publications

 (29)
PMCID: 5893770
PMID: 29670644
DOI: 10.3389/fgene.2018.00107

[…] single-locus analysis (fujisawa and barraclough, ) but depends on the availability of additional data/analyses from independent characters (esselstyn et al., ). additionally, we used the bayesian poisson tree processes model (bptp) (zhang et al., ) in the bptp webserver (http://species.h-its.org/ptp/) under default parameters. bptp does not require an ultrametric gene tree and uses, instead, […]

PMCID: 5743570
PMID: 29299292
DOI: 10.1002/ece3.3554

[…] and coalescent (intraspecific) processes (generalized mixed yule coalescent model, pons et al., ; fujisawa & barraclough, ) or on branch length distributions on the phylogenetic tree (poisson tree processes model, zhang et al., )., previous studies have confirmed that dna barcoding can successfully discriminate echinoderm species (hoareau & boissin, ; layton, corstorphine, […]

PMCID: 5662090
PMID: 29084279
DOI: 10.1371/journal.pone.0186259

[…] values of 0.75, 1.0, and 1.5 were applied to assess the influence of this parameter on the number of entities recognized, with the number of iterations (20) and number of bins (20) held stable., the poisson tree processes (ptp) method models speciation using the number of substitutions inferred from branch lengths on a ml input tree []. two independent poisson processes are estimated […]

PMCID: 5644147
PMID: 29037251
DOI: 10.1186/s13071-017-2457-1

[…] parsimony and bayesian inference methods. molecular species delimitation was evaluated through pairwise intraspecific and interspecific distances, automatic barcode gap discovery, single-rate poisson tree processes and multi-rate poisson tree processes., both cox1 and gpi genes recognized and differentiated t. cruzi, trypanosoma cruzi marinkellei, trypanosoma dionisii and trypanosoma […]

PMCID: 5629031
PMID: 28982192
DOI: 10.1371/journal.pone.0186140

[…] and with a minimum percentage of identity (i.e. 99%) and then motu were identified for each gene and the concatenated information. in addition, species delimitation analysis was performed with the poisson tree processes (ptp) including a bayesian implementation of the model [], using the phylogenetic consensus tree based on the concatenated genetic datasets. the estimations were made using […]


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PTP 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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