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Protocols

jMOTU specifications

Information


Unique identifier OMICS_15065
Name jMOTU
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input format FASTA, NEXUS
Operating system Unix/Linux
Programming languages Java
Computer skills Medium
Version 1.0.7
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Mark Blaxter

Publication for jMOTU

jMOTU citations

 (26)
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Conserved community structure and simultaneous divergence events in the fig wasps associated with Ficus benjamina in Australia and China

2018
BMC Ecol
PMCID: 5883542
PMID: 29615023
DOI: 10.1186/s12898-018-0167-y
call_split See protocol

[…] ances []. COI K2P distances were calculated [in Mesquite; ] for congeneric sister clades of wasps from different continents. We then further tested these species hypotheses on COI sequences using the jMOTU software package [] that is designed to cluster sequences according to a range of cut-off values—an inflection point in jMOTU outputs purportedly shows the barcoding gap. […]

library_books

Genetic Variation of the Endangered Neotropical Catfish Steindachneridion scriptum (Siluriformes: Pimelodidae)

2018
Front Genet
PMCID: 5827538
PMID: 29520295
DOI: 10.3389/fgene.2018.00048

[…] equences used in this study was OT = 0.0079 (0.79%) of divergence. From the set of the genus Steindachneridion sequences available on BOLD, three MOTUs were identified using the OT value and software jMOTU: S. scriptum from the UUR, S. scriptum from the UPR, and S. parahybae. The COI inter-MOTU between S. scriptum from the UUR and S. scriptum from the UPR showed values larger than the OT (mean 0.0 […]

library_books

Coalescent based delimitation outperforms distance based methods for delineating less divergent species: the case of Kurixalus odontotarsus species group

2017
Sci Rep
PMCID: 5700917
PMID: 29170403
DOI: 10.1038/s41598-017-16309-1

[…] lated sequences; instead uncorrected p-distances should be used,,.Secondly, a method of fixed threshold was performed to cluster the COI sequences into molecular operational taxonomic units (MOTU) in jMOTU. The value of low blast identity filter was set to 97% according to the user guide and the value of minimum alignment length in base pairs was set to 658 bp because COI sequences obtained from G […]

library_books

A Comprehensive Quality Evaluation System for Complex Herbal Medicine Using PacBio Sequencing, PCR Denaturing Gradient Gel Electrophoresis, and Several Chemical Approaches

2017
Front Plant Sci
PMCID: 5601397
PMID: 28955365
DOI: 10.3389/fpls.2017.01578

[…] into four categories, including (1) tree-based methods, e.g., neighbor joining, maximum likelihood, ATIM and SAP; (2) similarity-based methods, e.g., nearest-neighboring (NN), BLAST, TaxI, BRONX and jMOTU; (3) character-based diagnostics, e.g., BLOG and DNA-BAR; and (4) statistical methods. Several studies were found reporting the comparison of these different analysis methods (; ; ; ). Yet, the […]

call_split

Capture efficiency and trophic adaptations of a specialist and generalist predator: A comparison

2017
Ecol Evol
PMCID: 5395461
PMID: 28428866
DOI: 10.1002/ece3.2812
call_split See protocol

[…] sing MAFFT (Katoh & Standley, ), and the sequences with indels causing frameshifts were also removed. The remaining haplotypes were clustered into MOTUs (=molecular operational taxonomic units) using jMOTU 4.1 (Jones, Ghoorah, & Blaxter, ) with a 4‐bp cutoff. Each MOTU was compared to the GenBank database (http://blast.ncbi.nlm.nih.gov/Blast.cgi) using megablast, to the BOLD database (http://www.b […]

library_books

The golden mimicry complex uses a wide spectrum of defence to deter a community of predators

2017
eLife
PMCID: 5295815
PMID: 28170317
DOI: 10.7554/eLife.22089.019

[…] es) were removed. Furthermore, sequences with stop codons and indels causing frameshifts were also removed. Remaining haplotypes were clustered into molecular operational taxonomic units (MOTU) using jMOTU 4.1 () with a 4 bp cut-off (corresponding to 3% sequence divergence). Each MOTU was compared to the GenBank database using megablast and BOLD database and to the sequences of mimics obtained wit […]

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jMOTU institution(s)
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
jMOTU funding source(s)
Supported by the Leverhulme Trust (F/00158/BS).

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