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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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  • person_outline Fabian Klötzl <>
  • person_outline Bernhard Haubold <>

Publication for ANchor DIstances

andi in publications

 (4)
PMCID: 5913888
PMID: 29685100
DOI: 10.1186/s12864-018-4680-3

[…] 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 […]

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

[…] 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 […]

PMCID: 4810242
PMID: 26959064
DOI: 10.3390/life6010011

[…] tree and support values from the output of dnadist using the program consense, which is part of the phylip package [].subject a to pairwise bootstrap analysis as implemented in the latest version of andi [] and also calculate the consensus tree using consense.use afra to carry out quartet analysis on andi-distances computed from a.for each cluster in the consensus tree, extract the three support […]

PMCID: 4825649
PMID: 26837952
DOI: 10.1534/g3.115.025197

[…] gene selection did not affect the final tree topology (data not shown). to verify that concatenation did not adversely affect our tree construction, we used the whole genome phylogenetic software andi (). the entire de novo assembly fasta files for each isolate were used as input for this analysis. the resulting distance matrix was plotted as a tree using r. haplotype networks were drawn […]


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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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