Aliscore protocols

Aliscore specifications

Information


Unique identifier OMICS_08061
Name Aliscore
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Patrick Kück <>

Publication for Aliscore

Aliscore IN pipelines

 (10)
2014
PMCID: 4040987
PMID: 24732282
DOI: 10.1093/gbe/evu078

[…] taxon, and 4) have a median of <2 sequences per taxon. sequences of each accepted cluster were aligned using clustal omega (sievers et al. 2011). ambiguously aligned regions were removed using aliscore and alicut (kück 2009; misof and misof 2009). maximum-likelihood (ml) phylogenetic trees were inferred individually for each gene cluster with raxml 7.3.2 (stamatakis 2006) using […]

2013
PMCID: 3794015
PMID: 24130664
DOI: 10.1371/journal.pone.0072855

[…] material s1. each gene was aligned separately using the muscle algorithm (muscle version 3.6, [87]) and checked manually. ambiguously aligned or randomly similar sequence sections were detected with aliscore [88] and removed. the final, concatenated data set contained 5742 bp (including gaps). parameters for the substitution model (gtr+g) were estimated separately for each gene by partitioning […]

2013
PMCID: 3856133
PMID: 24350268
DOI: 10.1155/2013/407072

[…] from the main analyses., single alignments (per fragment) were created with mafft version 6.847b [30] with the implemented e-ins-i algorithm. alignments of 16s, 18s, and 28s rrna were masked with aliscore version 5.1 [17, 31] by running 10,000,000,000 replicates. all ambiguous positions were automatically cut with alicut version 2.0 [17, 31] to remove highly variable positions that could lead […]

2013
PMCID: 4225663
PMID: 24238092
DOI: 10.1186/1471-2148-13-253

[…] groups of 58 species were aligned with mafft using the most accurate option l-ins-i [67,68]. to increase the signal-to-noise ratio, sections with random sequence similarity were identified with aliscore version 1.0 [69,70] and subsequently excluded with alicut [71]. we constructed individual trees for each protein using a parallel pthreads-based version of raxml version 7.7.1 [72,73] […]

2011
PMCID: 3123331
PMID: 21731644
DOI: 10.1371/journal.pone.0021031

[…] iterative progressive algorithm which outperformed other methods in benchmark tests [31], [32]. each of the three sequence alignments (18s, 28s, and ef1af2) was screened for randomised sections with aliscore [17] using all possible pairwise comparisons and a window size w = 6. within aliscore, gaps were treated as ambiguous characters. randomised sections (28s rrna: 725 base positions (bp); 18s […]

Aliscore institution(s)
Zoologisches Forschungsmuseum A Koenig, Bonn, Germany and Biozentrum Grindel und Zoologisches Museum, Universität Hamburg, Hamburg, Germany

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