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Opal specifications

Information


Unique identifier OMICS_03738
Name Opal
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Protein and DNA sequences
Input format FASTA
Output data Protein and DNA alignments
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 2.1.3
Stability Stable
Maintained Yes

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Publication for Opal

Opal in publications

 (13)
PMCID: 5723593
PMID: 29238535
DOI: 10.1002/ece3.3525

[…] as the reference sequence from the king cobra were aligned using the saté iterative alignment program (liu et al., ) with mafft (katoh, kuma, toh, & miyata, ; katoh & toh, ) as the aligner, opal (wheeler & kececioglu, ) as the merger, fasttree (price, dehal, & arkin, ) as the tree estimator, and other parameters under the default saté‐ii‐fast settings. the sequences assembled […]

PMCID: 5397798
PMID: 28435440
DOI: 10.1186/s13015-017-0102-3

[…] set for which the aligner yields the computed alignment of highest estimated accuracy., in our parameter advising experiments, we assess the true accuracy of the multiple sequence alignment tool opal [, ] combined with an advisor that uses the accuracy estimator facet [] (the best estimator for parameter advising in the literature), augmented by our new coreness predictor as well as by two […]

PMCID: 5123300
DOI: 10.1186/s12864-016-3101-8

[…] a set of subset msas. then, every pair of subset alignments that are adjacent to each other in the tree are merged into a larger alignment using a profile-profile alignment technique (default is opal []). this produces a set of larger subset alignments that overlap and agree pairwise in all homologies for those sequences that they share and enables an alignment on the entire set […]

PMCID: 5076506
PMID: 27507814
DOI: 10.1074/jbc.M116.733675

[…] (kansas university) provided a software expansion that allowed amino acid sequences as input for saté analysis. parameters for saté were: maximum subproblem size, 20% of data set; merger algorithm, opal (); tree estimator, raxml (); number of cpus used, 2; alignment algorithm, mafft (); break strategy, centroid; and iteration limit, 20 after best maximum likelihood score. run time for the saté […]

PMCID: 4938164
PMID: 27391450
DOI: 10.1371/journal.pone.0159131

[…] likelihood phylogeny were created with one representative sequence from each of the 106, 539 bacteria otus using practical alignment using saté and transitivity (pasta) [] with the mafft aligner [], opal merger [], and fasttree tree estimation [] algorithms. sequences were deposited in the ncbi sequence read archive (sra) under accession number (srx766152)., we measured a broad range […]


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Opal institution(s)
Department of Computer Science, The University of Arizona, Tucson, AZ, USA
Opal funding source(s)
This project was supported by a PhD Fellowship from the University of Arizona National Science Foundation IGERT Genomics Initiative grant DGE-0114420 and the US National Science Foundation through grant DBI-0317498.

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