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andi specifications

Information


Unique identifier OMICS_09287
Name andi
Alternative name ANchor DIstances
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA
Operating system Unix/Linux
Programming languages C
License GNU General Public License version 2.0
Computer skills Advanced
Version 0.12
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Fabian Klötzl
  • person_outline Bernhard Haubold

Publication for ANchor DIstances

andi citations

 (7)
library_books

Comparative genomics of the wheat fungal pathogen Pyrenophora tritici repentis reveals chromosomal variations and genome plasticity

2018
BMC Genomics
PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] ts were viewed in IGV [], Tablet version 1.16.09.06 [] and SAMtools Tview version 0.1.19-96b5f2294a [].Genome nucleotide pairwise distance was calculated with GenomeTools version 1.5.8 genomediff []. Andi [], with Kimura modelling and anchor pair significance of 0.05 was also used for calculating genomic distances and 1000-time bootstrap. Whole genome phylogenetic trees were constructed using Phyl […]

library_books

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

2018
Wellcome Open Res
PMCID: 5930550
PMID: 29774245
DOI: 10.21956/wellcomeopenres.15526.r32391

[…] tationally feasible due to the slow mapping step (using bowtie2) not being parallelisable by strain.We also created pairwise distance matrices using: Mash v1.0 (default settings) between assemblies. Andi v0.9.2 (default settings) between assemblies.Hamming distance between informative k-mers using a subsample of 1% of counted k-mers from assemblies .Hamming distance between SNP sites produced by […]

library_books

Method for the Identification of Taxon Specific k mers from Chloroplast Genome: A Case Study on Tomato Plant (Solanum lycopersicum)

2018
Front Plant Sci
PMCID: 5776150
PMID: 29387080
DOI: 10.3389/fpls.2018.00006

[…] ces we used to find k-mers are in Supplementary Data ). The tree was constructed using the computer program MEGA version 6 () and was based on a distance matrix constructed using the computer program andi () to get an overview of the available data. The phylogenetic tree of Solanaceae is a subtree from the constructed tree.To identify S. lycopersicum specific k-mers, we used different GenomeTester […]

library_books

Antibiotic resistance potential of the healthy preterm infant gut microbiome

2017
PeerJ
PMCID: 5270596
PMID: 28149696
DOI: 10.7717/peerj.2928

[…] ding summarised contigs extracted per sample. As a reference, all S. aureus complete genomes were downloaded from PATRIC (Release May 2016), totalling 118 genomes.An anchor based phylogenetic method, andi (v.0.10) (), was used to estimate the evolutionary distances between the study and global S. aureus genomes set, using PHYLIP (v.3.696) () to infer the neighbour-joining phylogeny. Following asse […]

library_books

Support Values for Genome Phylogenies

2016
Life
PMCID: 4810242
PMID: 26959064
DOI: 10.3390/life6010011

[…] of 3085 genomes of Streptococcus pneumoniae, which were sequenced in the course of a pneumococcal outbreak []. We calculated the corresponding pairwise distance matrix and neighbor-joining tree using andi in 4:37 h. Quartet analysis then took 2:18 h and occupied 150 MB of memory. This shows that quartet analysis scales well to large datasets. […]

library_books

Global MLST of Salmonella Typhi Revisited in Post genomic Era: Genetic Conservation, Population Structure, and Comparative Genomics of Rare Sequence Types

2016
Front Microbiol
PMCID: 4774407
PMID: 26973639
DOI: 10.3389/fmicb.2016.00270

[…] l S. Typhi genomes. To compute large genome samples is computationally demanding, time-consuming and technically challenging. Therefore, we utilized a newer approach of alignment-free algorithm using andi v1.4 () to rapidly compute large-scale evolutionary distances between 1,808 S. Typhi (∼8.6 Gbases; six genomes were excluded from phylogenetic analyses due to low quality) and bias from mapping a […]


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andi institution(s)
Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany; Institue for Neuro- and Bioinformatics, Lübeck University, Lübeck, Germany; Mathematical Stochastics, Mathematical Institute, Freiburg University, Germany
andi funding source(s)
Supported by the Deutsche Forschungsgemeinschaft through grant Pf672/3-1.

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