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Protocols

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


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Documentation


Maintainer


This tool is not available anymore.

Publication for Poisson Tree Processes

PTP citations

 (68)
library_books

Hidden diversity: Phylogeography of genus Ototyphlonemertes Diesing, 1863 (Ototyphlonemertidae: Hoplonemertea) reveals cryptic species and high diversity in Chilean populations

2018
PLoS One
PMCID: 5919620
PMID: 29698411
DOI: 10.1371/journal.pone.0195833

[…] ith 5,000 bootstraps replicates.The resulting trees from RAxML analyses of single and concatenated markers were used as input to estimate species delimitation using the Bayesian implementation of the Poisson Tree Processes (bPTP software, available at the web-service http://species.h-its.org/) [] with 5,000 MCMC generations, 100 thinnings and a burn-in of 0.1. Since bPTP analysis from COX3 did not […]

call_split

Little Divergence Among Mitochondrial Lineages of Prochilodus (Teleostei, Characiformes)

2018
Front Genet
PMCID: 5893770
PMID: 29670644
DOI: 10.3389/fgene.2018.00107
call_split See protocol

[…] for 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, a […]

library_books

Detection of sister species in invasive populations of the fall armyworm Spodoptera frugiperda (Lepidoptera: Noctuidae) from Uganda

2018
PLoS One
PMCID: 5882101
PMID: 29614067
DOI: 10.1371/journal.pone.0194571

[…] and were potentially introduced to Africa as a single event.Dumas et al. [] using multiple molecular species delimiting methods, including the Generalized Mixed Yule Coalescent approach [, ] and the Poisson-Tree-Processes [], found statistical support for the presence of two sister S. frugiperda species, broadly grouped into either the rice-preferred (MF197867, this study) or the corn-preferred ( […]

library_books

Phylogenomics and barcoding of Panax: toward the identification of ginseng species

2018
BMC Evol Biol
PMCID: 5883351
PMID: 29614961
DOI: 10.1186/s12862-018-1160-y

[…] ate species discrimination []. Recently proposed methods include the Generalized Mixed Yule Coalescent (GMYC) [], Bayesian species identification using the multispecies coalescent (MSC) model [], and Poisson Tree Processes (PTP, mPTP) [, ]. Despite constant methodological improvements, there is no silver bullet for species delimitation and concerns have been raised that species delimitation approa […]

library_books

Phylogeography and DNA based species delimitation provide insight into the taxonomy of the polymorphic rose chafer Protaetia (Potosia) cuprea species complex (Coleoptera: Scarabaeidae: Cetoniinae) in the Western Palearctic

2018
PLoS One
PMCID: 5819786
PMID: 29462164
DOI: 10.1371/journal.pone.0192349

[…] or visualization of possible phylogeographic patterns. For insect mtDNA this analysis split the haplotypes into subgroups (separated networks) and usually joins haplotypes above the species-level [–].Poisson Tree Processes (PTP) and Automatic Barcode Gap Discovery (ABGD) were used to delimitate species for separate gene datasets. In PTP, the Yule-coalescent transition points that mark species boun […]

library_books

DNA barcoding of reef brittle stars (Ophiuroidea, Echinodermata) from the southwestern Indian Ocean evolutionary hot spot of biodiversity

2017
Ecol Evol
PMCID: 5743570
PMID: 29299292
DOI: 10.1002/ece3.3554

[…] (interspecific) 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, & Hebert, […]


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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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