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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

Versioning


No version available

Maintainer


  • person_outline Patrick Kück <>

Publications for Aliscore

Aliscore citations

 (33)
library_books

Genome sequencing of Rhinorhipus Lawrence exposes an early branch of the Coleoptera

2018
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 […]

library_books

Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution

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 […]

library_books

Complete mitochondrial genomes from two species of Chinese freshwater crabs of the genus Sinopotamon recovered using next generation sequencing reveal a novel gene order (Brachyura, Potamidae)

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 […]

library_books

Deep level phylogeny of Cicadomorpha inferred from mitochondrial genomes sequenced by NGS

2017
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 […]

library_books

Mitochondrial Genome Assemblies of Elysia timida and Elysia cornigera and the Response of Mitochondrion Associated Metabolism during Starvation

2017
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 […]

library_books

Core column prediction for protein multiple sequence alignments

2017
PMCID: 5397798
PMID: 28435440
DOI: 10.1186/s13015-017-0102-3

[…] from further analysis; and (b) those that compute a column quality score, which can be thresholded. tools that simply mask unreliable columns of an alignment include gblocks [], trimal [], and aliscore []. popular quality-score tools are noisy [], zorro [], tcs [], and guidance []., our experiments compare our coreness predictor to tcs and zorro: the most recent tools that provide quality […]


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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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