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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 citations

 (25)
library_books

Comparative Genomic Analysis of Acanthamoeba Endosymbionts Highlights the Role of Amoebae as a “Melting Pot” Shaping the Rickettsiales Evolution

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. […]

library_books

Determinants of the Efficacy of Natural Selection on Coding and Noncoding Variability in Two Passerine Species

2017
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>  […]

library_books

Gene duplication and co evolution of G1/S transcription factor specificity in fungi are essential for optimizing cell fitness

2017
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 […]

library_books

Core column prediction for protein multiple sequence alignments

2017
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 […]

library_books

SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter

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, […]

library_books

The genome of the emerging barley pathogen Ramularia collo cygni

2016
PMCID: 4979122
PMID: 27506390
DOI: 10.1186/s12864-016-2928-3

[…] the 31 downloaded fungal genomes plus r. collo-cygni were identified using the orthomcl output. single copy genes were identified and aligned using mafft linsi []. the alignments were masked using zorro [] with a cutoff value of 4.0 and checked for recombination using phipack [] with default settings. after the recombination test 1251 alignments remained. two taxa, cochliobolus carbonum […]


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

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