QUOTA-ALIGN specifications

Information


Unique identifier OMICS_14737
Name QUOTA-ALIGN
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Stability Stable
Requirements
GLPK
Maintained Yes

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Documentation


Maintainer


  • person_outline Haibao Tang <>

Publication for QUOTA-ALIGN

QUOTA-ALIGN in publications

 (14)
PMCID: 5577786
PMID: 28854926
DOI: 10.1186/s12915-017-0412-4

[…] and between amaranth and beet (ref-beet1.1; []) chromosomes were identified and investigated using the recommended parameters (dagchainer = relative gene order and merge syntenic blocks = quota align) of the coge [] synmap [] tool. in short, synmap uses last [] to identify homologous genes between the designated chromosomes and dagchainer [] to identify collinear blocks of homologous […]

PMCID: 5529502
PMID: 28747711
DOI: 10.1038/s41598-017-06929-y

[…] using the synmap utility of the coge website (https://genomevolution.org/coge/). the syntenic blocks containing multiple genes were detected using apgv3 cds data with default settings except for the quota align merge algorithm, and the final syntenic gene-set output with gevo links was downloaded for further analysis., the regression analysis was performed using the r function lm on genes, […]

PMCID: 5529103
PMID: 28746368
DOI: 10.1371/journal.pone.0181669

[…] chains of syntenic genes, the dagchainer module (with the ‘relative gene order’ option activated and the ‘maximum distance between two matches’ parameter set to 20) was used in conjunction with the quota-align algorithm (with the maximum distance between two blocks set to 20 genes), both of which are implemented within the coge synmap function. the chromosomal locations of ohnologous […]

PMCID: 5133247
PMID: 27994606
DOI: 10.3389/fpls.2016.01778

[…] wgd gene pairs were identified as deriving from α or β musa wgd using available α and β blocks (). additional paralogous relationships were detected using synmap with default parameters and a 3 to 3 quota-align ratio for banana (). gene scale duplications corresponding to two consecutive duplicated genes (tandem duplications) and duplicated genes separated by twenty or fewer gene loci (proximal […]

PMCID: 5033976
PMID: 27721818
DOI: 10.3389/fpls.2016.01424

[…] within the complete genome sequence, dagchainer software (with the ‘relative gene order’ option activated and the ‘maximum distance between two matches’ parameter set to 20) was used together with quota-align algorithm (with maximum distance between two blocks set to 20 genes), both implemented to the synmap function within coge. the chromosomal locations of the ohnolog bahd genes […]


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QUOTA-ALIGN institution(s)
Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA; iPlant, Department of Plant Sciences, University of Arizona, Tucson, USA; Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA
QUOTA-ALIGN funding source(s)
This work was supported by the US National Science Foundation (MCB-0820821, MCB-0821096 and DBI-0849896).

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