TOPALi protocols

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Associated diseases

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TOPALi specifications

Information


Unique identifier OMICS_04247
Name TOPALi
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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Maintainers


  • person_outline TOPALi <>
  • person_outline Iain Milne <>

Publications for TOPALi

TOPALi in pipelines

 (7)
2017
PMCID: 5271407
PMID: 28095503
DOI: 10.1371/journal.pntd.0005297

[…] bartonella amplified from the sample emg01 are available in genbank at #kx377404 and #kx377405., phylogeny of the detected bartonella with other members of the bartonella genus was established with topali 2.5 software (biomathematics and statistics scotland, edinburgh, uk). available sequences of ftsz, glta and rpob genes of validated bartonella species were retrieved from the national center […]

2016
PMCID: 4734696
PMID: 26828867
DOI: 10.1371/journal.pone.0148430

[…] accession number: jx512682, jx512672, jx512671, jx512705, jx512677, jx494371, jx272795, jx272796, jx494370, jx494372, jx494375, jx512703 and jx512694., a phylogenetic tree was constructed in topali v2 software, [] using a maximum likelihood algorithm, evolution model gtr+g with bootstrap analysis for 1000 replicates. the candida albicans its sequence (accession number kp131664) was used […]

2015
PMCID: 4981918
PMID: 26607216
DOI: 10.1111/mec.13434

[…] using muscle (edgar ). the alignment was used to construct a bayesian phylogeny with 2 million generations. model selection (f81) and molecular phylogenetic construction was carried out using topali (milne et al. ). the phylogenetic tree was mid‐point rerouted and formatted in figtree v1.4 (http://tree.bio.ed.ac.uk/software/figtree/). for each barcode pair, the number of reads […]

2014
PMCID: 4065256
PMID: 24760389
DOI: 10.1534/g3.114.010660

[…] and plugins therein. amino acid alignments were carried out using the muscle plugin (). the bayesian trees were constructed using the jtt + i + γ model for amino acid substitution predicted by topali v2. in , 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 from chicken, […]

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

[…] sequences were aligned using clustal omega program []. the program bioedit [] was used to assess the nature of variability and the entropy of the alignment among the species. the program topali v.2.5 [] 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, and bayesian […]


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TOPALi in publications

 (135)
PMCID: 5908196
PMID: 29630596
DOI: 10.1371/journal.pgen.1007322

[…] the ncbi taxonomy browser., protein sequences from the nine species that belonged to the same gh family were aligned using clustalw [] and subjected to phylogenetic analysis with phyml embedded in topali v 2.5 []. to retrieve the respective closest pcwdcazyme neighbors from other fungi, one or more trichoderma proteins from each gh protein family (including pl1 and aa9 auxiliary proteins) […]

PMCID: 5893783
PMID: 29670859
DOI: 10.3389/fcimb.2018.00097

[…] phylogenetic tree was obtained for the concatenated alignment with phyml 3.0 (guindon and gascuel, ), using the most appropriate model of nucleotide substitution and likelihood scores assessed by topali v2.5 (milne et al., ) and by jmodeltest (posada, ). the best model was determined by using the akaike information criterion (aic) (akaike, ; posada and buckley, ). supports for the nodes […]

PMCID: 5848442
PMID: 29530098
DOI: 10.1186/s13071-018-2694-y

[…] [] were loaded into the mega7 software []. phylogenetic relationships of the haplotypes were inferred by coalescent simulations using median-joining model implemented in network 5.0 [, ]. the topali v2.5 software [] was used to select a nucleotide substitution model with the best fit to the aligned sequences dataset and to construct the phylogenetic trees using the bayesian inference […]

PMCID: 5834606
PMID: 29500409
DOI: 10.1038/s41467-018-03294-w

[…] with uncertain heterozygous sites (<0.70 posterior probability threshold) were coded with iupac symbols. tests for recombination using the difference of sums-of-squares method were implemented in topali v1 (sliding window 100 bp, 10 bp step size, 0.5 threshold); these tests found no evidence for recombination in the eight nuclear introns examined in this study., double-digest rad seq (ddrad) […]

PMCID: 5821490
PMID: 29492455
DOI: 10.1126/sciadv.aao1261

[…] and goldman (wag) substitution model and taking into account among-site rate heterogeneity with four γ-distributed categories. the bi phylogenies were calculated using mrbayes implemented in the topali v2.5 package (). the bi analyses were based on the wag substitution model taking into account the among-site rate heterogeneity with four γ-distributed categories. posterior probability […]


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

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