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jPHYDIT specifications


Unique identifier OMICS_08892
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Stability No
Maintained No


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jPHYDIT citations


Screening, isolation and molecular identification of biodegrading mycobacteria from Iranian ecosystems and analysis of their biodegradation activity

PMCID: 5607059
PMID: 28933031
DOI: 10.1186/s13568-017-0472-4

[…] sequences were aligned manually with all existing sequences of the closely related mycobacteria retrieved from the genbanktm database, compared with the relevant sequences and analyzed using the jphydit program (jeon et al. )., the genbank accession numbers for the 16s rrna sequencing of the mycobacteria isolated in this study are; m. coockii like (jx566888), m. simiae (kf028776), m. […]


Metabolic response induced by parasitic plant fungus interactions hinder amino sugar and nucleotide sugar metabolism in the host

Sci Rep
PMCID: 5124995
PMID: 27892480
DOI: 10.1038/srep37434

[…] and no. 11. for phylogenetic analysis, sequences obtained in this study and sequences of gymnosporangium species in the genbank sequence database were aligned and compared by pairwise alignment using jphydit. molecular sequence data from these aecial specimens were confirmed by comparison with previously published south korean specimens in the genbank database (fj848744, fj848745, fj848746, 630 bp […]


Prevalence of Non Tuberculous Mycobacteria in Hospital Waters of Major Cities of Khuzestan Province, Iran

PMCID: 4829604
PMID: 27148491
DOI: 10.3389/fcimb.2016.00042

[…] with 72°c for 5 min., the sequences of rpob gene for each isolate were aligned separately and compared with all existing relevant sequences of mycobacteria recovered from genbank database using jphydit program (jeon et al., ). percentages of similarity between sequences of each gene were determined by comparing sequences to an in-house database of rpob sequences. phylogenetic trees […]


Non contiguous finished genome sequence and description of the gliding bacterium Flavobacterium seoulense sp. nov.

Stand Genomic Sci
PMCID: 4286143
PMID: 25584140
DOI: 10.1186/1944-3277-9-34

[…] analysis was performed using the 16s rrna gene sequences of strain em1321t and related species. sequences were aligned according to the bacterial rrna secondary structure model using the jphydit []. phylogenic trees were constructed using neighbor-joining (nj) and maximum-likelihood (ml) methods implemented in mega version 5 []. the resultant tree topologies were evaluated […]


First Report of Ceriporiopsis resinascens (Phanerochaetaceae, Basidiomycota) in South Korea

PMCID: 3749423
PMID: 23983553
DOI: 10.4489/MYCO.2009.37.4.305

[…] kit (bioneer). sequencing was performed using the aforementioned primers on an abi 3730xl automated sequencer (applied biosystems, usa). the its sequence was proofread and edited using the jphydit program () and then deposited in genbank (accession number gu080235). phylogenetic trees were inferred from sequence alignment using the neighbor-joining (nj), maximum parsimony (mp) […]


An enhanced RNA alignment benchmark for sequence alignment programs

Algo Mol Biol
PMCID: 1635699
PMID: 17062125
DOI: 10.1186/1748-7188-1-19

[…] computationally demanding. consequently, researchers often create an initial sequence alignment that is afterwards corrected manually or by the aid of rna alignment editors (e. g. construct [], jphydit [], ralee [], or sarse []) to satisfy known structural constraints. the question which alignment technique and/or program performs best under which conditions has been extensively […]

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jPHYDIT institution(s)
Interdisciplinary Program in Bioinformatics, Seoul National University Shilim-dong, Kwanak-gu, Seoul, Korea; School of Biological Sciences, Seoul National University Shilim-dong, Kwanak-gu, Seoul, Korea

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