ZORRO protocols

View ZORRO computational protocol

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ZORRO specifications

Information


Unique identifier OMICS_08068
Name ZORRO
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Perl
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for ZORRO

ZORRO in pipelines

 (8)
2017
PMCID: 5395668
PMID: 28420738
DOI: 10.1128/mBio.00413-17

[…] sequence set to representative consensus sequences. following dereplication, this set of consensus sequences was aligned with muscle (, ). probabilistic masking of the alignment was performed with zorro (). a final tree was created using fasttree (). assignment of each of the 990 uclust nonredundant lineages to one of these 17 sfam families was done using a “majority rules” approach, […]

2017
PMCID: 5751055
PMID: 29177480
DOI: 10.1093/gbe/evx246

[…] (), and homologs from all complete bacterial, archaeal, viral, and eukaryotic genomes were retrieved by blastp (e-value cutoff 1e-15). protein sequences were aligned using mafft () and trimmed using zorro with a probability cutoff of 0.4 as suggested (). phylogenetic trees were constructed using raxml with the best model selected by the program () and were scanned for a bipartition […]

2017
PMCID: 5751055
PMID: 29177480
DOI: 10.1093/gbe/evx246

[…] all complete bacterial and archaeal genomes were retrieved by blastp search (e-value cutoff 1e-15). protein sequences were aligned using mafft () and ambiguously aligned columns were trimmed using zorro with a probability cutoff of 0.4 as suggested (). phylogenetic trees were constructed using raxml with the best model selected by the program (). gene families with spurious alignment (e.g. […]

2016
PMCID: 4907049
PMID: 27296936
DOI: 10.1186/s12864-016-2738-7

[…] inflation parameter, selecting groups containg bidirectional best hits and no paralogs. blast settings were as found in [], with an e-value threshold of 0.1. protein alignments were masked with zorro to reduce noise from uninformative amino acid alignment positions and checked for a best fit among protein evolution models with prottest version 3.1 [, ]. the best-fit protein evolution model […]

2015
PMCID: 4432239
PMID: 25987870
DOI: 10.3897/zookeys.500.9360

[…] alignment using fast fourier transform, http://www.ebi.ac.uk/tools/msa/mafft/) using the default settings. an alignment mask excluding sites of uncertain positional homology was generated using zorro (). zorro uses a pair hidden markov model and a weighted sum of pairs scheme (guided by a reference tree) that sums up the probability that a given alignment column appears over the total […]


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ZORRO in publications

 (22)
PMCID: 5751055
PMID: 29177480
DOI: 10.1093/gbe/evx246

[…] all complete bacterial and archaeal genomes were retrieved by blastp search (e-value cutoff 1e-15). protein sequences were aligned using mafft () and ambiguously aligned columns were trimmed using zorro with a probability cutoff of 0.4 as suggested (). phylogenetic trees were constructed using raxml with the best model selected by the program (). gene families with spurious alignment (e.g. […]

PMCID: 5714183
PMID: 29045655
DOI: 10.1093/gbe/evx213

[…] last accessed october 20, 2017) identifier was inconsistent between species. the orthologous gene triplets were then aligned using muscle (). regions with poor alignment quality were identified using zorro () and were removed, resulting in the removal of 17% of sites. we then estimated dn and ds using paml (one-ratio model) () and excluded triplets with extreme substitution rate estimates (dn>  […]

PMCID: 5448814
PMID: 28505153
DOI: 10.1371/journal.pgen.1006778

[…] retrieved as previously described []. the phylogenetic analysis was performed on an alignment build using mafft-l-ins-i (-maxiterate 1000) [, ] we then used probabilistic alignment masking using zorro to create different datasets with varying score thresholds, where the top 20% scoring columns was chosen as the best alignment (). next, we used prottest 3 to determine the empirical amino-acid […]

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

[…] a column quality score, which can be thresholded. tools that simply mask unreliable columns of an alignment include gblocks [], trimal [], and aliscore []. popular quality-score tools are noisy [], zorro [], tcs [], and guidance []., our experiments compare our coreness predictor to tcs and zorro: the most recent tools that provide quality scores, as opposed to masking columns. among […]

PMCID: 5395668
PMID: 28420738
DOI: 10.1128/mBio.00413-17

[…] sequence set to representative consensus sequences. following dereplication, this set of consensus sequences was aligned with muscle (, ). probabilistic masking of the alignment was performed with zorro (). a final tree was created using fasttree (). assignment of each of the 990 uclust nonredundant lineages to one of these 17 sfam families was done using a “majority rules” approach, […]


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ZORRO institution(s)
Department of Biology, University of Virginia, Charlottesville, VA, USA

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