TOPALi protocols

TOPALi specifications


Unique identifier OMICS_04247
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 2.5
Stability Stable
Maintained Yes


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  • person_outline TOPALi <>
  • person_outline Iain Milne <>

Publications for TOPALi

TOPALi IN pipelines

PMCID: 4065256
PMID: 24760389
DOI: 10.1534/g3.114.010660

[…] plugins therein. amino acid alignments were carried out using the muscle plugin (edgar 2004). the bayesian trees were constructed using the jtt + i + γ model for amino acid substitution predicted by topali v2. in figure 1, we used human rhodopsin as an out-group (nm_001131055.1), and also included biogenic amine receptors including aminergic, serotonin, dopamine, and histamine h2 receptors […]

PMCID: 3852316
PMID: 24350255
DOI: 10.1155/2013/289285

[…] sequences were aligned using clustal omega program [17]. the program bioedit [18] was used to assess the nature of variability and the entropy of the alignment among the species. the program topali v.2.5 [19] was used to select the best substitution model and the best method for phylogenetic tree reconstruction based on akaike information criterion, corrected aicc1 and aicc2, […]

TOPALi institution(s)
Scottish Crop Research Institute, Invergowrie, Dundee, UK

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