Aliscore protocols

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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

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Maintainer


  • person_outline Patrick Kück <>

Publication for Aliscore

Aliscore in pipelines

 (8)
2017
PMCID: 5330476
PMID: 28245223
DOI: 10.1371/journal.pone.0172352

[…] in iq-tree as well []. alternative analytic scenarios were generated, including best-fit partition scheme (partitionfinder 2.0 []) and filtered potential non-phylogenetic genetic information using aliscore (default parameters []); in all cases phylogenetic inferences were calculated with iq-tree as detailed above (see for a summary and comparison with main ml result)., to evaluate the d. […]

2017
PMCID: 5644144
PMID: 29041914
DOI: 10.1186/s12864-017-4197-1

[…] a second one with partitions based on protein domain-boundaries. for both datasets, we identified randomly similar aligned sites within each msas of each orthologous gene using a modified version of aliscore (v1.2) [, , ], with the same settings described previously []. for the dataset based on gene-boundaries, we removed ambiguously aligned sections with the aid of alicut (v2.3) [], replaced […]

2017
PMCID: 5674035
PMID: 29118611
DOI: 10.3897/zookeys.705.11852

[…] the iterative refinement method g-ins-i (accurate alignment), in which the gap opening and extension penalties were 1.53 and 0.123, respectively. ambiguous or randomly similar sites were removed by aliscore 2.0 (; ) using default settings. these aa alignments were later used as a backbone to align the corresponding nucleotide (nt) sequences using dambe 5.3.15 (). all 13 pcgs alignments […]

2015
PMCID: 4494064
PMID: 25977457
DOI: 10.1093/gbe/evv090

[…] in subsequent analyses of pectinase families, we aligned the amino acid sequences using mafft l-ins-i (; ). poorly aligned regions of each gene were masked using alicut v2.0 () after detection with aliscore v2.3 (window size = six) (; ; ). the concatenated matrix “all-w6,” produced by fasconcat v1.0 (), included 40 taxa and 28,807 amino acid sites from 136 genes. to evaluate the phylogeny […]

2014
PMCID: 4040987
PMID: 24732282
DOI: 10.1093/gbe/evu078

[…] <5 sequences per taxon, and 4) have a median of <2 sequences per taxon. sequences of each accepted cluster were aligned using clustal omega (). ambiguously aligned regions were removed using aliscore and alicut (; ). maximum-likelihood (ml) phylogenetic trees were inferred individually for each gene cluster with raxml 7.3.2 () using the best-fitting amino acid substitution model […]


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Aliscore in publications

 (32)
PMCID: 5930637
PMID: 29743928
DOI: 10.1186/s12983-018-0262-0

[…] using blosum62 distance scores [] and following the methods reported by misof et al. []. we used pal2nal [] to generate multiple sequence alignments of nucleotides corresponding to amino acids and aliscore 2.0 [, ] to identify random similarity within alignments which were removed using alicut 2.3 (https://github.com/mptrsen/scripts/blob/master/alicut_v2.3.pl)., the matrix of all 4220 […]

PMCID: 5644144
PMID: 29041914
DOI: 10.1186/s12864-017-4197-1

[…] a second one with partitions based on protein domain-boundaries. for both datasets, we identified randomly similar aligned sites within each msas of each orthologous gene using a modified version of aliscore (v1.2) [, , ], with the same settings described previously []. for the dataset based on gene-boundaries, we removed ambiguously aligned sections with the aid of alicut (v2.3) [], replaced […]

PMCID: 5674035
PMID: 29118611
DOI: 10.3897/zookeys.705.11852

[…] the iterative refinement method g-ins-i (accurate alignment), in which the gap opening and extension penalties were 1.53 and 0.123, respectively. ambiguous or randomly similar sites were removed by aliscore 2.0 (; ) using default settings. these aa alignments were later used as a backbone to align the corresponding nucleotide (nt) sequences using dambe 5.3.15 (). all 13 pcgs alignments […]

PMCID: 5585334
PMID: 28874826
DOI: 10.1038/s41598-017-11132-0

[…] codes through degen v1.4 (degen-code), ; (3) pcgdegenrna: 13 protein-coding genes with degen-coding combined with 24 rna genes. additionally, the datasets of pcg and pcgrna were masked by using aliscore version 2.0, , combined with alicut version 2.0, . finally, to investigate the potential long-branch effect on the tree topology, a series of reduced datasets (i.e. 43 taxa datasets without […]

PMCID: 5534330
DOI: 10.1093/gbe/evx129

[…] 8.0.3 (biomatters, new zeeland, ) and using siphonaria pectinata (ay345049) as the outgroup. alignments were performed using fast fourier transform (mafft; ) with the g-insi mode, inspected by aliscore () and conspicuous sites removed. all individual alignments were concatenated and a phylogenetic reconstruction performed using raxml () with the lg + i+g + f model (four discrete gamma […]


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

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