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AliGROOVE specifications

Information


Unique identifier OMICS_15833
Name AliGROOVE
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.05
Stability Stable
Requirements
PERL
Maintained Yes

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Maintainer


  • person_outline Patrick Kück

Publication for AliGROOVE

AliGROOVE citations

 (7)
library_books

Mitochondrial phylogenomics of Hemiptera reveals adaptive innovations driving the diversification of true bugs

2017
PMCID: 5597834
PMID: 28878063
DOI: 10.1098/rspb.2017.1223

[…] when analysing genomic data and ancient events [,,–]. the heterogeneity of sequence divergence within the dataset (e.g. each codon position of pcg and sequences of rna genes) was analysed using aligroove [] with the default sliding window size. indels in the nucleotide dataset were treated as ambiguity and a blosum62 matrix was used as the default amino acid substitution matrix. to account […]

library_books

Data on taxonomic status and phylogenetic relationship of tits

2016
PMCID: 5192249
PMID: 28050581
DOI: 10.1016/j.dib.2016.11.079

[…] method, c: 37 mitochondrial genes with the third sites of protein-coding genes not using ry-coding method plus one control region, d: five nuclear segments, were used to analyze the heterogeneity in aligroove , and the results can be found in . the best schemes were analyzed by using partitionfinder v1.1.1 , and the results were in . the gene trees in were constructed by using raxml 7.0.3 , […]

library_books

Genome analysis revealed novel genotypes and recombination of the human parechoviruses prevalent in children in Eastern China

2016
PMCID: 5100207
PMID: 27826360
DOI: 10.1186/s13099-016-0135-z

[…] with 1000 bootstrap resamples of the alignment data sets was generated using the neighbor-joining method in mega5.0 []. sequence divergence based on the complete genome of hpevs was analyzed using aligroove software []. the scores were ranging from −1, indicating full random similarity, to +1, non-random similarity., detection of potential recombinant sequences, identification of potential […]

library_books

Multiple Lines of Evidence from Mitochondrial Genomes Resolve Phylogenetic Relationships of Parasitic Wasps in Braconidae

2016
Genome Biol Evol
PMCID: 5630901
PMID: 27503293
DOI: 10.1093/gbe/evw184

[…] window and a monte carlo resampling approach to detect strongly divergent nucleotide sequences that could have the potential to bias tree reconstruction and nodal support; this was implemented in aligroove version 1.05 (). each partition defined by gene and codon position was assessed by aligroove employing default settings. there is no specific criterion on which to base the inclusion […]

library_books

Capturing the Phylogeny of Holometabola with Mitochondrial Genome Data and Bayesian Site Heterogeneous Mixture Models

2016
Genome Biol Evol
PMCID: 4898802
PMID: 27189999
DOI: 10.1093/gbe/evw086

[…] of 10,076 bp); and 5) the aa matrix, including amino acid sequences of protein-coding genes (total of 3,723 amino acids). the heterogeneity of sequence divergence within data sets was analyzed using aligroove () with the default sliding window size. indels in nucleotide data set were treated as ambiguity and a blosum62 matrix was used as default amino acid substitution matrix. the metric […]

library_books

Ancient horizontal gene transfer and the last common ancestors

2015
BMC Evol Biol
PMCID: 4427996
PMID: 25897759
DOI: 10.1186/s12862-015-0350-0

[…] [-]). generally, these programs identify columns in an alignment that fail a statistical test, resulting in them being removed before phylogenetic analyses are performed. some algorithms, such as aligroove, also detect and mask poorly aligned sites at the individual taxon level []. however, as suggested by wu et al. [], these global column-specific approaches may mask well-aligned, […]


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AliGROOVE institution(s)
Zoologisches Forschungsmuseum A. Koenig, Bonn, Germany; University of Amsterdam, Amsterdam, Netherlands

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