kmacs statistics

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kmacs specifications

Information


Unique identifier OMICS_05426
Name kmacs
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data DNA sequences
Input format FASTA
Output data A distance matrix
Output format PHYLIP
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Chris-André Leimeister <>

Information


Unique identifier OMICS_05426
Name kmacs
Interface Web user interface
Restrictions to use None
Input data DNA sequences
Input format FASTA
Output data A distance matrix
Output format PHYLIP
Programming languages C++
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Chris-André Leimeister <>

Publication for kmacs

kmacs in publications

 (4)
PMCID: 5610321
PMID: 28939913
DOI: 10.1038/s41598-017-12493-2

[…] of substrings in a pair of sequences. these algorithms are mostly used for string processing in computer science, like average common substring (acs), k-mismatch average common substring approach (kmacs). thirdly, methods based on information theory include global and local characterization of sequences and estimate genome entrop to regions. among them base-base correlation (bbc), information […]

PMCID: 5011920
PMID: 27602058
DOI: 10.1186/s13072-016-0085-1

[…] package software (http://www.tbi.univie.ac.at/rna/ [last accessed: 20/04/2016]) and completed in illustrator cs6 (adobe). a k-mer-based alignment-free sequence comparison was performed using kmacs (http://kmacs.gobics.de/ [last accessed: 20/04/2016])., a phrap assembly (http://www.phrap.org/phredphrapconsed.html; phrap version 1.090518) was generated from a randomly selected subset […]

PMCID: 4929450
PMID: 27363362
DOI: 10.1038/srep28970

[…] in inferring phylogenetic trees quickly and accurately from genome-scale data., we investigated nine af phylogenetic methods:  , co-phylog, cvt, ffp and spaced based on word count, and acs, gram, kmacs and kr based on match length (see ). the distance matrix generated by each of these methods was used to infer phylogenetic relationships using neighbour-joining. as a measure of accuracy […]

PMCID: 4918981
PMID: 27336403
DOI: 10.1371/journal.pcbi.1004985

[…] in the one sequence the shortest prefix that is absent from the other (called shustrings). ua uses a scoring function on matching statistics between unique, independent subwords. k-mismatch acs (kmacs) [] is an extension of the acs approach which approximates the number of substring matches with up to k mismatches. another, more recent extension of the acs approach is alfred-g, also capable […]


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kmacs institution(s)
Department of Bioinformatics, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany; Laboratoire Statistique et Génome, Université d’Évry Val d’Essonne, UMR CNRS 8071, USC INRA, Évry, France

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