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ModelGenerator specifications

Information


Unique identifier OMICS_13074
Name ModelGenerator
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Gene family alignment
Input format FASTA, PHYLIP
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 0.851
Stability Stable
Requirements
PAL
Source code URL http://mcinerneylab.com/wp-content/uploads/2011/09/modelgenerator_v_851.zip
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Thomas M Keane

Publication for ModelGenerator

ModelGenerator citations

 (189)
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Gene refashioning through innovative shifting of reading frames in mosses

2018
Nat Commun
PMCID: 5908804
PMID: 29674719
DOI: 10.1038/s41467-018-04025-x
call_split See protocol

[…] a maximum likelihood method using PhyML 3.1 and a distance method using neighbor of PHYLIP-3.695. The optimal model of amino acid substitution and rate heterogeneity was chosen based on the result of ModelGenerator. […]

call_split

Cameroonian fruit bats harbor divergent viruses, including rotavirus H, bastroviruses, and picobirnaviruses using an alternative genetic code

2018
Virus Evol
PMCID: 5888411
PMID: 29644096
DOI: 10.1093/ve/vey008
call_split See protocol

[…] g Fast Fourier Transform) (for Picobirnaviridae and Partiviridae, because of the high genetic diversity in these families) (). After trimming with trimAL (), substitution models were determined using ModelGenerator () and phylogenetic trees constructed using RAxML (), with the autoMRE flag, which enables a posteriori bootstopping analysis. All trees were visualized in FigTree (http://tree.bio.ed.a […]

call_split

Selection, periodicity and potential function for Highly Iterative Palindrome 1 (HIP1) in cyanobacterial genomes

2018
Nucleic Acids Res
PMCID: 5861425
PMID: 29432573
DOI: 10.1093/nar/gky075
call_split See protocol

[…] nii ATCC 35469) were used to root the tree (not shown). Multiple sequence alignments were constructed using MUSCLE (), followed by manual refinement. Model selection was performed in TOPALi 2.5 using ModelGenerator (); the best model was GTR+I+Γ according to the Akaike Information Criteria (AIC1 and AIC2). The resulting phylogeny (Figure ) is in agreement with recently published cyanobacterial phy […]

library_books

Genome Wide Identification, Evolutionary and Expression Analyses of the GALACTINOL SYNTHASE Gene Family in Rapeseed and Tobacco

2017
Int J Mol Sci
PMCID: 5751367
PMID: 29261107
DOI: 10.3390/ijms18122768

[…] Gamma distribution parameter α: 0.43) and 100 bootstrap replicates and was used to infer evolutionary relationships among the sequences. The model used for ML and Bayesian trees were calculated using ModelGenerator v0.85 (http://mcinerneylab.com/software/modelgenerator/). There are 56 nucleotides and 96 amino acid substitution models in the Model generator. The optimal model will be selected based […]

call_split

Central European Woolly Mammoth Population Dynamics: Insights from Late Pleistocene Mitochondrial Genomes

2017
Sci Rep
PMCID: 5735091
PMID: 29255197
DOI: 10.1038/s41598-017-17723-1
call_split See protocol

[…] es–,–, were downloaded from the NCBI SRA database, and the consensus sequences generated here were aligned with these using ‘Consensus Align’ in Geneious vR8. Evolutionary models were estimated using modelgenerator v85, jModelTest2 v2.1.10 and IQ-Tree v1.4.2, and phylogenetic analysis performed using Geneious vR8 for Neighbour Joining, MEGA for Maximum Parsimony, IQ-Tree v1.4.2 for Maximum Likelih […]

library_books

A novel type I cystatin of parasite origin with atypical legumain binding domain

2017
Sci Rep
PMCID: 5727476
PMID: 29235483
DOI: 10.1038/s41598-017-17598-2

[…] nalysis contained 15 unambiguously aligned protein sequences, each 102 amino acids long (Supplementary Information, ). Optimal parameters (α = 1.26) and evolution model (LG + G) were calculated using ModelGenerator v. 0.851 and applied during a Bayesian inference and a Maximum likelihood analysis. Both methods provided trees with similar topologies. We therefore present the Bayesian inference tree […]

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ModelGenerator institution(s)
Bioinformatics Laboratory, Department of Biology, National University of Ireland, Maynooth, Co. Kildare, Ireland; Bork Group, EMBL Heidelberg, Heidelberg, Germany; Department of Computer Science, University College London, Gower Street, London, UK; Department of Computer Science, National University of Ireland, Maynooth, Co. Kildare, Ireland
ModelGenerator funding source(s)
This work was support by the Irish Research Council for Science, Engineering and Technology (IRCSET).

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