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MitoPhAST, a new automated mitogenomic phylogeny tool in the post-genomic era with a case study of 89 decapod mitogenomes including eight new freshwater crayfish mitogenomes

Overview of attention for article published in Molecular Phylogenetics & Evolution, April 2015
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Citations

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56 Mendeley
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Title
MitoPhAST, a new automated mitogenomic phylogeny tool in the post-genomic era with a case study of 89 decapod mitogenomes including eight new freshwater crayfish mitogenomes
Published in
Molecular Phylogenetics & Evolution, April 2015
DOI 10.1016/j.ympev.2015.02.009
Pubmed ID
Authors

Mun Hua Tan, Han Ming Gan, Mark B. Schultz, Christopher M. Austin

Abstract

The increased rate at which complete mitogenomes are being sequenced and their increasing use for phylogenetic studies have resulted in a bioinformatic bottleneck in preparing and utilising such data for phylogenetic analysis. Hence, we present MitoPhAST, an automated tool that 1) identifies annotated protein-coding gene features and generates a standardised, concatenated and partitioned amino acid alignment directly from complete/partial GenBank/EMBL-format mitogenome flat files, 2) generates a maximum likelihood phylogenetic tree using optimised protein models and 3) reports various mitochondrial genes and sequence information in a table format. To demonstrate the capacity of MitoPhAST in handling a large dataset, we used 81 publicly available decapod mitogenomes, together with eight new complete mitogenomes of Australian freshwater crayfishes, including the first for the genus Gramastacus, to undertake an updated test of the monophyly of the major groups of the order Decapoda and their phylogenetic relationships. The recovered phylogenetic trees using both Bayesian and ML methods support the results of studies using fragments of mtDNA and nuclear markers and other smaller-scale studies using whole mitogenomes. In comparison to the fragment-based phylogenies, nodal support values are generally higher despite reduced taxon sampling suggesting there is value in utilising more fully mitogenomic data. Additionally, the simple table output from MitoPhAST provides an efficient summary and statistical overview of the mitogenomes under study at the gene level, allowing the identification of missing or duplicated genes and gene rearrangements. The finding of new mtDNA gene rearrangements in several genera of Australian freshwater crayfishes indicates that this group has undergone an unusually high rate of evolutionary change for this organelle compared to other major families of decapod crustaceans. As a result, freshwater crayfishes are likely to be a useful model for studies designed to understand the evolution of mtDNA rearrangements. We anticipate that our bioinformatics pipeline will substantially help mitogenome-based studies increase the speed, accuracy and efficiency of phylogenetic studies utilising mitogenome information. MitoPhAST is available for download at https://github.com/mht85/MitoPhAST.

Twitter Demographics

The data shown below were collected from the profiles of 6 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 56 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Germany 2 4%
United States 1 2%
Austria 1 2%
Brazil 1 2%
Unknown 51 91%

Demographic breakdown

Readers by professional status Count As %
Researcher 19 34%
Student > Ph. D. Student 10 18%
Student > Bachelor 6 11%
Student > Master 6 11%
Professor 5 9%
Other 3 5%
Unknown 7 13%
Readers by discipline Count As %
Agricultural and Biological Sciences 32 57%
Biochemistry, Genetics and Molecular Biology 10 18%
Earth and Planetary Sciences 2 4%
Computer Science 2 4%
Environmental Science 1 2%
Other 1 2%
Unknown 8 14%

Attention Score in Context

This research output has an Altmetric Attention Score of 3. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 07 November 2019.
All research outputs
#8,395,475
of 16,164,081 outputs
Outputs from Molecular Phylogenetics & Evolution
#2,391
of 3,633 outputs
Outputs of similar age
#83,434
of 218,467 outputs
Outputs of similar age from Molecular Phylogenetics & Evolution
#38
of 65 outputs
Altmetric has tracked 16,164,081 research outputs across all sources so far. This one is in the 47th percentile – i.e., 47% of other outputs scored the same or lower than it.
So far Altmetric has tracked 3,633 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 6.1. This one is in the 33rd percentile – i.e., 33% of its peers scored the same or lower than it.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 218,467 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 61% of its contemporaries.
We're also able to compare this research output to 65 others from the same source and published within six weeks on either side of this one. This one is in the 38th percentile – i.e., 38% of its contemporaries scored the same or lower than it.