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phyutility specifications


Unique identifier OMICS_21687
Name phyutility
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 2.7.1
Stability Stable
Maintained Yes




No version available


  • person_outline Stephen Smith

Publication for phyutility

phyutility citations


Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits

BMC Evol Biol
PMCID: 5932825
DOI: 10.1186/s12862-018-1142-0

[…] id not converge due to the position of the outgroup Trichoplax adhaerens. To estimate convergence for the cnidarian ingroup, we removed T. adhaerens from all sampled trees using the prune function in Phyutility [] and reran bpcomp on both chains.We conducted character-mapping analyses under the explicit statistical models for character evolution described in SIMMAP and implemented in phytools [, , […]


Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics

Appl Plant Sci
PMCID: 5895186
PMID: 29732266
DOI: 10.1002/aps3.1036

[…] on of 0.3. All clusters containing sequences from at least eight species of 30 were selected and aligned with MAFFT v7.305b using the L‐INS‐I method (Katoh and Standley, ). Alignments were trimmed by phyutility (Smith and Dunn, ), and initial phylogenetic trees were estimated by RAxML v. 8.1.2 (Stamatakis, ). We selected the rooted tree approach of Yang and Smith (), used C. canadensis (redbud; Ce […]


Comparison of taxon‐specific versus general locus sets for targeted sequence capture in plant phylogenomics

Appl Plant Sci
PMCID: 5895190
PMID: 29732262
DOI: 10.1002/aps3.1032

[…] each sequence set, sequences were aligned with MAFFT (Katoh and Standley, ) using default parameters. Sites with more than 50% missing data were removed from alignments using the “clean” function in Phyutility (Smith and Dunn, ). Concatenated alignments were generated for each of the four locus sets using the “concat” function in Phyutility.Because a target locus might comprise multiple target se […]


Origin and evolution of the nuclear auxin response system

PMCID: 5873896
PMID: 29580381
DOI: 10.7554/eLife.33399.035

[…] sequences to ascertain orthology. MAFFT (ver7.123b; ) iterative refinement algorithm (E-INS-i) was used to align the CDS sequences. Alignment positions with more than 50% gaps were removed using the Phyutility program (ver2.2.6; before the phylogeny construction. PartitionFinder (ver1.1.1; ) was used to identify the most suitable evolutionary model for al […]


Two new species of Xanthagaricus and some notes on Heinemannomyces from Asia

PMCID: 5804139
PMID: 29559820
DOI: 10.3897/mycokeys.28.21029
call_split See protocol

[…] Each individual dataset, either ITS or 28S, was aligned in MAFFT v.6.8 () separately with default settings, and manually edited in BioEdit v.7.0.9 (). ITS and 28S datasets was then concatenated using Phyutility () for further phylogenetic analyses, and treated here as a ITS-28S dataset. The combined dataset (ITS-28S) was used for the recognition of the new species in Xanthagaricus and to find out […]


Genome Guided Phylo Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses

Sci Rep
PMCID: 5648822
PMID: 29051622
DOI: 10.1038/s41598-017-13236-z
call_split See protocol

[…] o orthologous sets for each gene and a multiple alignment was created using mafft,. In this way, the use of all-by-all BLAST and the MCL algorithm are completely avoided. After further filtering with phyutility and several scripts from Yang and Smith, concatenated trees, coalescence-based quartet summary species trees, and binned coalescence-based quartet summary trees were created using RAxML, AS […]


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phyutility institution(s)
Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
phyutility funding source(s)
Supported by NSF Cyberinfrastructure for Phylogenetic Research (CIPRES) grant EF-0331654.

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