DIVERGE protocols

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DIVERGE specifications

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Unique identifier OMICS_07161
Name DIVERGE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 3.0
Stability Stable
Maintained No

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Publications for DIVERGE

DIVERGE in pipelines

 (9)
2017
PMCID: 5748683
PMID: 29206198
DOI: 10.3390/genes8120365

[…] the positive selection of sabath genes using site models and branch-site models under the paml program. we also analyzed the functional divergence of sabath genes in s. miltiorrhiza using the diverge program. finally, we analyzed the tissue-specific expression of the sabath gene family in s. miltiorrhiza., the sabath gene family was first identified in arabidopsis, and twenty-four […]

2016
PMCID: 4825928
PMID: 27058959
DOI: 10.1371/journal.pgen.1005973

[…] of protein sequences were constructed with cobalt (www.ncbi.nlm.nih.gov/tools/cobalt) and manually modified. the analysis of type i and type ii functional divergence was performed with the diverge 3.0 software []. maximum likelihood (ml) phylogenies were estimated with phyml3.0 assuming 8 categories of γ-distributed substitution rate and sprs algorithms. for phylogeny of protein […]

2015
PMCID: 4470668
PMID: 26083253
DOI: 10.1371/journal.ppat.1004913

[…] of protein sequences were constructed with cobalt (www.ncbi.nlm.nih.gov/tools/cobalt) and manually modified. the analysis of type i and type ii functional divergence was performed with the diverge 3.0 software []. maximum likelihood (ml) phylogenies were estimated with phyml3.0 [] assuming 8 categories of γ-distributed substitution rate and sprs algorithms. for phylogeny of protein […]

2014
PMCID: 4018336
PMID: 24819937
DOI: 10.1371/journal.pone.0097425

[…] analysis by mapping their loci onto chromosomes in scale., functional divergences (type i and type ii) between clusters were tested using the gu99 and gu2013 probabilistic models implemented in the diverge 2.0 software , . pairwise coefficients (θij±se) and likelihood ratio statistics (lrt) for simian enteric or myeloid defensin clusters were analyzed using the bootstrapped gu99 probabilistic […]

2012
PMCID: 3413703
PMID: 22879944
DOI: 10.1371/journal.pone.0042336

[…] groups: conservation, probabilistic, and selection (). scorecons and consurf are measures of site-specific evolutionary conservation based on amino acid sequence comparisons; the polyphen2, sift, diverge and phastcons measures form a heterogeneous group with methods that measure site-specific evolution, or relative effects of site-specific changes, based on probabilistic analyses of multiple […]


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DIVERGE in publications

 (60)
PMCID: 5851622
PMID: 29538447
DOI: 10.1371/journal.pone.0194335

[…] alterations in gene function., functional divergence between four sub-families of eif2ak sequences and related kinase sequences is inferred by type i and type ii divergence analyses utilizing diverge 3.0[]. type i functional divergence suggests heterogeneous evolutionary rates between duplicated genes, while type ii functional divergence suggests radical changes to biochemical properties […]

PMCID: 5841269
PMID: 29552026
DOI: 10.3389/fgene.2018.00064

[…] determined to calculate the selection pressure and sliding window analysis was carried out to analyze the synonymous (ks) and non-synonymous (ka) rates of all sbp-box genes encoding sites paralogs., diverge 3.0 beta 1 software was used to examining functional divergence (i type ii type) among each subfamily of sbp genes according to constructed phylogenetic tree. after gene duplication type […]

PMCID: 5793430
PMID: 29390964
DOI: 10.1186/s12862-018-1129-x

[…] conserved amino acids are expected to have an important role in protein structure and function. therefore, changes at these sites may be an indicator of functional divergence. we used the software diverge v3.0 [], to examine site-specific shifted evolutionary rates by calculating the coefficient of type i of divergence (ɵi). type i of divergence results in differing functional constraints […]

PMCID: 5738429
PMID: 29263428
DOI: 10.1038/s41598-017-18196-y

[…] by natural selection. the ‘covarion’-type models, also known as type i functional divergence, detect differential rates (acceleration or deceleration) in each amino acid position. the software diverge 3.0 was used to detect the functional divergence among different subgenotypes and genotypes of csfv. the coefficients of type-i functional divergence (θi) were calculated. if θi […]

PMCID: 5748683
PMID: 29206198
DOI: 10.3390/genes8120365

[…] []. posterior probabilities (qks) were estimated with the bayes empirical bayes (beb) method []., an analysis of the functional divergence between the smsabath genes of subgroups was performed using diverge version 3.0 []. the method could estimate significant changes in the site-specific shifts, based on maximum likelihood procedures []. the estimation was based on the neighbor-joining tree, […]


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DIVERGE institution(s)
State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China

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