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MEGA-V specifications

Information


Unique identifier OMICS_14382
Name MEGA-V
Alternative name Mutation Enrichment Gene set Analysis of Variants
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A Boolean matrice of mutations.
Operating system Unix/Linux
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
shiny, mega, mega-v
Maintained Yes

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Documentation


Maintainer


  • person_outline Francesca Ciccarelli

Publication for Mutation Enrichment Gene set Analysis of Variants

MEGA-V citations

 (1763)
library_books

Architrypethelium murisporum (Ascomycota, Trypetheliaceae), a remarkable new lichen species from Thailand challenging ascospore septation as an indicator of phylogenetic relationships

2018
PMCID: 5958175
PMID: 29780270
DOI: 10.3897/mycokeys.25.23836

[…] oups to Architrypethelium () and two taxa of Bathelium madreporiforme were used as the outgroup. The DNA datasets (mtSSU and nuLSU) were aligned separately using MUSCLE () and improved manually using MEGA v.7 (). The nucleotide substitution model for maximum likelihood (ML) and Bayesian inference (BI) analyses was chosen using jModelTest v.2.1.4 () with the Akaike Information Criterion (AIC). The […]

call_split

Sporulation specific cell division defects in ylmE mutants of Streptomyces coelicolor are rescued by additional deletion of ylmD

2018
Sci Rep
PMCID: 5943314
PMID: 29743540
DOI: 10.1038/s41598-018-25782-1
call_split See protocol

[…] search the NCBI database (www.ncbi.nlm.nih.gov) using BLASTP against the non-redundant protein sequence database. Alignment of YlmD and YlmE was generated using ClustalW followed by manual editing in MEGA v. 4.0. The neighbour-joining trees were generated with default parameters settings as implemented in MEGA v. 4.0. The maximum-likelihood trees were made using the best fit models predicted by ME […]

library_books

Microbial community analysis and biodeterioration of waterlogged archaeological wood from the Nanhai No. 1 shipwreck during storage

2018
Sci Rep
PMCID: 5940862
PMID: 29740020
DOI: 10.1038/s41598-018-25484-8

[…] .cgi) and the GenBank database. Each isolate was compared against known taxa present in the database. Phylogenetic analyses were conducted using the Molecular Evolutionary Genetics Analysis software (MEGA, v. 6.06) using the neighbour-joining method. Confidence in tree topology was estimated using the bootstrap method (1,000 bootstrap replicates). […]

library_books

Widespread plant specialization in the polyphagous planthopper Hyalesthes obsoletus (Cixiidae), a major vector of stolbur phytoplasma: Evidence of cryptic speciation

2018
PLoS One
PMCID: 5940214
PMID: 29738577
DOI: 10.1371/journal.pone.0196969

[…] s performed on an ABI Prism 3700 automated sequencer (Macrogen Inc., Seoul, South Korea). Sequences were edited using FinchTV v.1.4.0 (http://www.geospiza.com) and aligned with ClustalW [] within the MEGA v.5.2 software []. Whenever possible, six specimens per each H. obsoletus population were genotyped for mitochondrial markers, (). The nomenclature of newly identified haplotypes followed the des […]

library_books

Multilevel social structure and diet shape the gut microbiota of the gelada monkey, the only grazing primate

2018
Microbiome
PMCID: 5935910
PMID: 29729671
DOI: 10.1186/s40168-018-0468-6

[…] in the “GUniFrac” package []. For constructing the phylogenies upon which the Unifrac distances were based, sequences were aligned using MUSCLE [] and a neighbor joining tree [] was constructed using MEGA v7.0.26 []. The phylogeny of OTUs classified to the phylum Fibrobacteres was constructed in the same fashion. Metagenomes were predicted using Phylogenetic Investigation of Communities by Reconst […]

call_split

Eight new Arthrinium species from China

2018
PMCID: 5945706
PMID: 29755262
DOI: 10.3897/mycokeys.34.24221
call_split See protocol

[…] Sequences generated from the forward and reverse primers were used to obtain consensus sequences using MEGA v. 6.0 (). The concatenated tree was inferred based ITS, TUB2 and TEF1 sequences (Figure ) using Bayesian and Maximum-likelihood analyses. Sequences were aligned using an online version of MAFFT […]

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MEGA-V institution(s)
Division of Cancer Studies, King’s College London, London, UK
MEGA-V funding source(s)
This work has been supported by the Biomedical Research Centre based at Guy’s and St Thomas’ NHS Foundation Trust and King’s College London.

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