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PUZZLE specifications


Unique identifier OMICS_32872
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Other
Computer skills Advanced
Stability Stable
Maintained Yes


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Publications for PUZZLE

PUZZLE citations


Considerations in computer aided design for inlay cranioplasty: technical note

PMCID: 5820390
PMID: 29313149
DOI: 10.1007/s10006-017-0668-4
call_split See protocol

[…] e cases with existing large defects or profound recession/displacement of the bone flap, tissue expansion may be indicated. Large defects are more easily approached using a segmented plate, with a 3D puzzle connection for reassembly (Fig. ), especially when PEEK is chosen as the material. PEEK implants are CNC-milled from rods that are 10, 15, or 18 cm in diameter. Two smaller plates are easier an […]


Is MMTV associated with human breast cancer? Maybe, but probably not

Virol J
PMCID: 5640909
PMID: 29029634
DOI: 10.1186/s12985-017-0862-x
call_split See protocol

[…] hbor Program (outgroup rooting and randomized input order options “on”). The majority rule consensus NJ trees were generated using the CONSENSE program. Additionally, the maximum-likelihood method in Puzzle 4.0 package was used []. Phylograms were visualized using Tree View []. Experimentally derived DNA were subjected to standard nucleotide BLAST searches (http://www.nebi.n/m.nih.gov/BLAST) to de […]


Cetaceans evolution: insights from the genome sequences of common minke whales

BMC Genomics
PMCID: 4311506
PMID: 25609461
DOI: 10.1186/s12864-015-1213-1

[…] opology optimization was chosen.NJ analysis [] was conducted using the PHYLIP package 3.69 [], based on Kimura’s [] two-parameter distance. Ts/Tv ratios (10.10) were estimated from the data set using PUZZLE 4.0.2 [] and then were used as inputs for the SEQBOOT, DNADIST, NEIGHBOUR, and CONSENS programs of the PHYLIP package. A bootstrap test (with 1,000 pseudoreplicates) [] was performed to determi […]


Characterization of the Complete Nuclear Ribosomal DNA Sequences of Paramphistomum cervi

Sci World J
PMCID: 4129167
PMID: 25140347
DOI: 10.1155/2014/751907
call_split See protocol

[…] ormed for each MP analysis. Bootstrap probability was calculated from 1,000 bootstrap replicates with 10 random additions per replicate in PAUP. A maximum likelihood (ML) analysis was performed using PUZZLE 4.1 []. A Bayesian inference (BI) was performed using MrBayes 3.1 [] with four independent Markov chains run for 1,000,000 metropolis-coupled Markov chain Monte Carlo generations and sampling a […]


In Vivo Time Resolved Microtomography Reveals the Mechanics of the Blowfly Flight Motor

PLoS Biol
PMCID: 3965381
PMID: 24667677
DOI: 10.1371/journal.pbio.1001823
call_split See protocol

[…] here). The picture is further complicated by the fact that b3, which is expected to act antagonistically with b1, also has higher amplitude oscillations on the high-amplitude wing ().To resolve this puzzle, we examined the movements of the basalare sclerite in greater depth. Our visualizations show that movement of the basalare sclerite is dominated by rotation about its external head on the low- […]


Evolutionary Reconstruction and Population Genetics Analysis of Aurora Kinases

PLoS One
PMCID: 3782425
PMID: 24086628
DOI: 10.1371/journal.pone.0075763

[…] lities (BP). The programs SEQBOOT and CONSENSE were used to estimate the confidence limits of branching points from 1000 bootstrap replications. ML tree topologies were constructed using the software PUZZLE 4.0 [], employing 1000 puzzling steps, the JTT substitution matrix, estimation of rate heterogeneity using the gamma distribution model with eight rate categories, and the gamma-parameter estim […]


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PUZZLE institution(s)
Zoologisches Institut, Universitat Munchen, Munich, Germany

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