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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


No version available

Maintainer


  • person_outline Patrick Kück

Publications for Aliscore

Aliscore citations

 (58)
library_books

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

2018
Front Zool
PMCID: 5930637
PMID: 29743928
DOI: 10.1186/s12983-018-0262-0

[…] es 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 orthologs a […]

call_split

Insight into higher level phylogeny of Neuropterida: Evidence from secondary structures of mitochondrial rRNA genes and mitogenomic data

2018
PLoS One
PMCID: 5790268
PMID: 29381758
DOI: 10.1371/journal.pone.0191826
call_split See protocol

[…] e compiled, namely with or without RNA genes.To reduce the random similarity in the sequence alignments, each alignment of protein-coding genes, tRNA genes and rRNA genes was individually masked with Aliscore version 2.0 [,]. The sequence alignments were screened separately with the following options: -r 2000, -w 6, -N, -o outgroups. Positions identified as randomly similar by Aliscore were remove […]

library_books

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

2017
BMC Genomics
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 ter […]

call_split

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
Zookeys
PMCID: 5674035
PMID: 29118611
DOI: 10.3897/zookeys.705.11852
call_split See protocol

[…] h 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 were comb […]

library_books

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

2017
Sci Rep
PMCID: 5585334
PMID: 28874826
DOI: 10.1038/s41598-017-11132-0

[…] guity 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 t […]

call_split

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

2017
Genome Biol Evol
PMCID: 5534330
DOI: 10.1093/gbe/evx129
call_split See protocol

[…] neious 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 categ […]

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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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