IQPNNI protocols

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IQPNNI specifications

Information


Unique identifier OMICS_15840
Name IQPNNI
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Windows
Programming languages C++
Computer skills Advanced
Stability No
Maintained No

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Publication for IQPNNI

IQPNNI in pipelines

 (4)
2013
PMCID: 3704272
PMID: 23442002
DOI: 10.1186/1471-2148-13-54

[…] cas1 until the end of csy4. nucleotide sequences from the resulting 19 strains were aligned using clustalw [] into an alignment of 8555 sites that is subsequently used for phylogeny estimation with iqpnni []., putative crispr arrays for the 19 strains are extracted using crisprfinder []. true crispr elements are found by comparing the repeat sequence to the known yersinia pestis repeat. […]

2013
PMCID: 3913041
PMID: 24075994
DOI: 10.1016/j.celrep.2013.08.031

[…] software (), correcting for multiple substitutions and bootstrapped by 1000 repetitions. for ml analysis, consensus trees were calculated, using tree-puzzle () (v5.3), from 100 trees generated with iqpnni () (v3.3.2) using the blosum62 substitution matrix and 4 categories of gamma-distributed substitution rates., pcr primers were designed using the probefinder v.2.45 (roche). the amplification […]

2010
PMCID: 3095337
PMID: 21106056
DOI: 10.1186/1471-2229-10-262

[…] genes in rice and arabidopsis, multiple sequence alignments were carried out using mafft [] and visualized using multiple align show http://www.bioinformatics.org/sms/multi_align.html. the program iqpnni [] was used to reconstruct a maximum likelihood phylogeny assuming the whelan and goldman model []. phylogenetic trees were finally visualized using the program geneious […]

2009
PMCID: 2771747
PMID: 19821963
DOI: 10.1186/1741-7007-7-68

[…] for further analysis that resulted in a significant hit for both domains., the 97 cyanobacterial tbdt sequences were aligned with mafft [] and a maximum likelihood tree was constructed with iqpnni v3.3.b4 []. as a substitution model we selected vt [] with gamma-distributed rate heterogeneity. support values were calculated from 1000 bootstrap replicates. the consensus tree […]


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IQPNNI in publications

 (14)
PMCID: 5796012
PMID: 29278391
DOI: 10.3390/ijms19010062

[…] algorithms [,,], particle swarm [], etc. besides these algorithms, there is much software, available online, based on a single criterion. for example, tnt [] and phylip [] are based on mp. raxml [], iqpnni [], mrbays [], garli [], and metapiga [] are based on ml. tnt implements different heuristic, such as sectorial and tree fusing, to address the inference of maximum parsimony trees., compared […]

PMCID: 4332441
PMID: 25564011
DOI: 10.1186/s13062-014-0031-8

[…] methods, we constructed unrooted maximum likelihood phylogenetic trees using the following procedure. given the nucleotide msas, neighbor-joining phylogenetic trees were obtained by iqpnni v 3.3 [] (nucleotide substitution model: general time reversible (gtr) model, bootstrap resampling: 1000 replicates). these neighbor-joining phylogenetic trees were used as starting trees […]

PMCID: 3913041
PMID: 24075994
DOI: 10.1016/j.celrep.2013.08.031

[…] software (), correcting for multiple substitutions and bootstrapped by 1000 repetitions. for ml analysis, consensus trees were calculated, using tree-puzzle () (v5.3), from 100 trees generated with iqpnni () (v3.3.2) using the blosum62 substitution matrix and 4 categories of gamma-distributed substitution rates. primers used in rt-pcr pcr primers were designed using the probefinder v.2.45 […]

PMCID: 3679003
PMID: 23776409
DOI: 10.1371/journal.pbio.1001585

[…] software , correcting for multiple substitutions and bootstrapped by 1,000 repetitions. for ml analysis, consensus trees were calculated (using tree-puzzle (v5.3)) from 100 trees generated with iqpnni (v3.3.2) using the blosum62 substitution matrix and four categories of gamma-distributed substitution rates. accession numbers of protein sequences used: q17053, p28682, p60015, p51476, […]

PMCID: 3267785
PMID: 22165866
DOI: 10.1186/1471-2105-12-470

[…] on phylogenomic datasets with missing data that contain more than 10,000 taxa. the concepts we introduce are generic, that is, they can be applied to other likelihood-based programs such as iqpnni [], garli [], phyml 3.0 [], fasttree 2.0 [], mrbayes [], phylobayes [], and beast [] or to libraries for computing the phylogenetic likelihood such as beagle […]


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IQPNNI institution(s)
Heinrich-Heine Universitat Dusseldorf, Germany; Forschungszentrum Julich, Germany

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