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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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This tool is not available anymore.

Publication for IQPNNI

IQPNNI citations

 (21)
library_books

Using MOEA with Redistribution and Consensus Branches to Infer Phylogenies

2017
Int J Mol Sci
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 to […]

library_books

A new ensemble coevolution system for detecting HIV 1 protein coevolution

2015
Biol Direct
PMCID: 4332441
PMID: 25564011
DOI: 10.1186/s13062-014-0031-8

[…] hylogenetic-based 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 in RA […]

call_split

Circadian and Circalunar Clock Interactions in a Marine Annelid

2013
Cell Rep
PMCID: 3913041
PMID: 24075994
DOI: 10.1016/j.celrep.2013.08.031
call_split See protocol

[…] X 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 (Roc […]

call_split

Co Expression of VAL and TMT Opsins Uncovers Ancient Photosensory Interneurons and Motorneurons in the Vertebrate Brain

2013
PLoS Biol
PMCID: 3679003
PMID: 23776409
DOI: 10.1371/journal.pbio.1001585
call_split See protocol

[…] talX 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, P06002 […]

call_split

Probabilistic models for CRISPR spacer content evolution

2013
BMC Evol Biol
PMCID: 3704272
PMID: 23442002
DOI: 10.1186/1471-2148-13-54
call_split See protocol

[…] f 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. The three […]

library_books

CodonPhyML: Fast Maximum Likelihood Phylogeny Estimation under Codon Substitution Models

2013
Mol Biol Evol
PMCID: 3649670
PMID: 23436912
DOI: 10.1093/molbev/mst034

[…] logeny inference. The only implementations offering a limited number of simple codon models for phylogeny estimation include MrBayes () and Beast (), which allow Bayesian estimation, and GARLI () and IQPNNI (; ), which perform tree estimation by the maximum likelihood (ML) criterion. However, the performance of tree inference under codon models (in terms of accuracy and speed) has not been documen […]

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

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