ALLMAPS protocols

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ALLMAPS specifications

Information


Unique identifier OMICS_07415
Name ALLMAPS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Haibao Tang <>

Information


Unique identifier OMICS_07415
Name ALLMAPS
Interface Web user interface
Restrictions to use None
Programming languages Python
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Haibao Tang <>

Publication for ALLMAPS

ALLMAPS in pipelines

 (2)
2018
PMCID: 5798813
PMID: 29423234
DOI: 10.1038/s41438-017-0011-0

[…] mentioned and then sorted in order of the location of the marker on the kim et al. genome sequence., marker alignment positions on the 10x scaffolds were converted into csv format for input into allmaps software for all four linkage maps (supplemental fileĀ ). interspecific linkage map files were modified to correct for a known translocation between chromosomes 1/8 between c. annuum and c. […]

2017
PMCID: 5240624
PMID: 28094805
DOI: 10.1038/srep40728

[…] proteins from the two species. we identified gene pairs that we were able to use for anchoring. the final pseudomolecule assembly was generated from the genetic map and synteny evidence using allmaps, where higher weighting was given to evidence from the genetic map. the macrosynteny between b. vulgaris and a. lyrata was compared by anchoring the genetic markers to the a. lyrata genome […]


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ALLMAPS in publications

 (11)
PMCID: 5798813
PMID: 29423234
DOI: 10.1038/s41438-017-0011-0

[…] mentioned and then sorted in order of the location of the marker on the kim et al. genome sequence., marker alignment positions on the 10x scaffolds were converted into csv format for input into allmaps software for all four linkage maps (supplemental fileĀ ). interspecific linkage map files were modified to correct for a known translocation between chromosomes 1/8 between c. annuum and c. […]

PMCID: 5723288
PMID: 29259619
DOI: 10.3389/fgene.2017.00180

[…] linkage groups of total lengths of 957, 1,017 and 919 cm, respectively. the anchored scaffolds were ordered and oriented according to the mapped position of the dna markers on the genetic maps using allmaps (tang et al., ), then obtained 9 pseudomolecules. whole genome synteny of the pseudomolecule to clementine (wu et al., ), pummelo and sweet orange (wang et al., ) were visualized […]

PMCID: 5765338
PMID: 29167271
DOI: 10.1534/g3.117.300196

[…] to 105 progeny isolates. linkage mapping was conducted in mapdisto v1.7.9 () as described in using a lod threshold of 5.0., p. teres f. teres isolate 0-1 assembled contigs were scaffolded using allmaps (). allmaps takes assembled contigs and generates scaffolds based on coordinates from genetic linkage maps, optical maps, or syntenic maps. to scaffold the 0-1 assembly, linkage maps […]

PMCID: 5824858
PMID: 28985339
DOI: 10.1093/dnares/dsx033

[…] missing genotypes. skewed markers were then added into the map by applying a multipoint maximum likelihood mapping. map distances were estimated using the kosambi mapping function. we then used the allmaps programme to construct melon pseudo-chromosomes based on a comparison between the constructed genetic map and the map of the melon genome. finally, we constructed pseudo-chromosomes referred […]

PMCID: 5432662
PMID: 28540183
DOI: 10.1016/j.gdata.2017.05.007

[…] that showed the highest sequence similarities with our assembled c. olitorius genome during the blast similarity search. for the construction of seven chromosome-scale pseudomolecules, we used allmaps to integrate the genome assembly with a rad-snp-based genetic map of c. olitorius ., the disease resistance-like (r-like) and defense response (dr) genes were manually categorized using […]


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ALLMAPS institution(s)
Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China; School of Plant Sciences, iPlant Collaborative, University of Arizona, Tucson, AZ, USA, IA, USA; J Craig Venter Institute, Chinakville, MD, USA; Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, USA, Ames, IA, USA; Department of Agronomy, Iowa State University, Ames, IA, USA; Heilongjiang River Fisheries Research Institute, Harbin, China

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