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Phycas specifications


Unique identifier OMICS_13189
Name Phycas
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Nucleotide sequence data
Output data Phylogenetic trees
Output format NEXUS
Operating system Mac OS, Windows
Programming languages C++, Python
Computer skills Advanced
Version 2.2.0
Stability Stable
Source code URL
Maintained Yes


No version available



  • person_outline Paul Lewis

Publication for Phycas

Phycas citations


Molecular approaches uncover cryptic diversity in intertidal Ligia isopods (Crustacea, Isopoda, Ligiidae) across the southern Africa coastline

PMCID: 5911383
PMID: 29686947
DOI: 10.7717/peerj.4658

[…] Γ model. We produced a majority-rule consensus tree of all bootstrap replicates using the Sumtrees command of DendroPy v4.1.0 ().We carried out Bayesian phylogenetic searches in MrBayes v3.2.5 () and Phycas v2.2.0 (). Searches in MrBayes consisted of two simultaneous searches of four chains, each sampled every 5,000th tree, while Phycas searches consisted of a single search, sampled every 50th tre […]


Out of Asia: mitochondrial evolutionary history of the globally introduced supralittoral isopod Ligia exotica

PMCID: 5853605
PMID: 29576934
DOI: 10.7717/peerj.4337
call_split See protocol

[…] hyML v3.0_360 () as implemented in a public server ( Bayesian Inference (BI), MrBayes v.3.2.6 (; ; ) as implemented in CIPRES, and Phycas v.1.2.0 () implemented locally, were employed. To alleviate the unpredictable behavior in Bayesian analysis when dealing with hard polytomies (i.e., “star-tree paradox”), which can lead to arbi […]


Cryptic biodiversity and phylogeographic patterns of Seychellois Ligia isopods

PMCID: 5633021
PMID: 29018626
DOI: 10.7717/peerj.3894
call_split See protocol

[…] an Inference. Parameters used in MrBayes v3.1.2 (; ) searches are presented in . All other parameters used were as default. We also carried out Bayesian searches implementing polytomy priors () under Phycas v2.2.0 () as to ensure that support values produced by MrBayes were not overestimated (i.e., “star-tree paradox”) (). We determined if Bayesian analyses had reached stationarity prior to estima […]


Phylogeographic patterns of a lower intertidal isopod in the Gulf of California and the Caribbean and comparison with other intertidal isopods

Ecol Evol
PMCID: 5214745
PMID: 28070297
DOI: 10.1002/ece3.2599

[…] th the SumTrees script of DendroPy v.3.10.1 (Sukumaran & Holder, ). Bayesian analyses were performed within MrBayes v.3.2.1 (Huelsenbeck & Ronquist, ; Ronquist & Huelsenbeck, ; Ronquist et al., ) and Phycas v.1.2.0 (Lewis, Holder, & Swofford, ), implementing the polytomy prior (Lewis, Holder, & Holsinger, ) in the latter. The polytomy prior is one of the proposed ways to address problems arising f […]


Evaluation of properties over phylogenetic trees using stochastic logics

BMC Bioinformatics
PMCID: 4908722
PMID: 27301397
DOI: 10.1186/s12859-016-1077-7

[…] itable for solving temporal and probabilistic problems in the domain of phylogenetics. Current probabilistic model checking tools are generic and powerful enough for our proposal. Other tools such as Phycas [], RevBayes [] or Beast2 [] are focused on solving a set of specific problems while our approach can answer a wider range of questions.The advantages of applying the probabilistic continuous-t […]


Conflicting genomic signals affect phylogenetic inference in four species of North American pines

PMCID: 4866652
PMID: 27060161
DOI: 10.1093/aobpla/plw019

[…] Species trees were reconstructed using the Bayesian method BEST (ver. 2.3) () with partitioning by-gene. To account for potential polytomies, and thus potential for the star tree paradox (; ), we ran Phycas (ver. 1.2.0) (), also a Bayesian method, with partitioning by-gene-site. We then analysed each gene separately using GARLI and MrBayes (partitioning by-site). The MrBayes outputs were further i […]


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Phycas institution(s)
Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA; Department of Ecology and Evolution, University of Kansas, Lawrence, KS, USA; Department of Biology, Duke University, Durham, NC, USA
Phycas funding source(s)
This project was supported by the National Science Foundation (grants No. EF-0331495, No. DEB-1036448, and No.DEB-1354146) and the Alfred P. Sloan Foundation (grant No. 98-4-5 ME), the National Science Foundation grant No. DEB-0732920, the National Evolutionary Synthesis Center, the National Science Foundation grant No. EF-0423641 and the Department of Ecology and Evolutionary Biology at the University of Kansas.

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