SDT protocols

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SDT specifications

Information


Unique identifier OMICS_06325
Name SDT
Alternative name Sequence Demarcation Tool
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Sequence Demarcation Tool

SDT in pipelines

 (15)
2018
PMCID: 5869529
PMID: 29562672
DOI: 10.3390/v10030136

[…] bootstrap replicates and the resulting trees were visualized in figtree (version 1.4.2) []. branches that had less than 50% bootstrap support were collapsed. sequence identity analysis using the sequence demarcation tool (sdt) (version 1.2) [] was carried out on the aligned amplicon clusters of each viral rna segment., full length genome sequences of the australian apmv isolate k75 and pdv […]

2017
PMCID: 5478126
PMID: 28632759
DOI: 10.1371/journal.pone.0179284

[…] 1000 bootstrap replicates. the resulting trees were visualized in figtree version 1.4.2 [] and branches that had less than 90% bootstrap support were collapsed. sequence identity analysis using the sequence demarcation tool (sdt) (version 1.2) [] was carried out on the aligned amplicon clusters of each rna and also on each of the individual amplicon clusters., haplotype networks were created […]

2017
PMCID: 5518176
PMID: 28744371
DOI: 10.1093/ve/vex017

[…] walking at macrogen inc. (south korea)., to investigate the anellovirus diversity detected in seals, the pairwise identities of the anellovirus genomes and orf1 sequences were determined using sdt v1.2 (). all anellovirus sequences with a detectable complete orf1 were downloaded from genbank (on the 18th of march 2017). 727 orf1 sequences (including 152 from this study) were translated, […]

2017
PMCID: 5632515
PMID: 29026649
DOI: 10.1093/ve/vex027

[…] romania)., viral orfs were predicted using a custom, papillomavirus-specific annotation tool as described previously (). genome-wide identity analysis was performed using default settings within sdt v1.2 (). pairwise sequence comparisons with papv1 () were performed within geneious version 10.2 (). the annotated sequence of papv1 was downloaded from the pave database (; ). the l-ins-i […]

2016
PMCID: 4748293
PMID: 26861415
DOI: 10.1038/srep20783

[…] and pcoa such that each dataset contributes equally to the distance calculated. average pairwise identities of rbcl sequences were determined at amino acid level for each environmental type using sequence demarcation tool (sdt) v1.2. variation of g+c percentage in each dataset was calculated using bioedit v7.0. test for natural selection pressures on form id rbcl sequences for each dataset […]


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SDT in publications

 (42)
PMCID: 5920176
PMID: 29700141
DOI: 10.1128/genomeA.00240-18

[…] phocoena) (), and burmeister’s porpoise (phocoena spinipinnis) (). the l1 gene sequence of the bdpv was compared to those of all cetacean pvs and the type species of the other 46 pv genera using the sequence demarcation tool (). the bdpv displayed greatest nucleotide identity (75.8%) to omikronpv1 (tursiops truncatus papillomavirus 6 [ttpv6]) (). given that this is the ninth pv type described […]

PMCID: 5890292
PMID: 29632309
DOI: 10.1038/s41598-018-23739-y

[…] and the resulting contigs were checked by blast for known virus sequences and obvious contamination by plant, microbe or human sequences., phylogenetic analyses were conducted in mega7 and sdt v. 1.2. multialignments were done using muscle as implemented in geneious or mega7. a maximum likelihood tree (100 bootstrap repetitions) was constructed by phyml with the gtr + g + i […]

PMCID: 5923437
PMID: 29565808
DOI: 10.3390/v10040143

[…] estimated via bootstrap replicates. phylogenetic trees were visualized using figtree 1.4.2 (http://tree.bio.ed.ac.uk/software/figtree/). nucleotide divergence calculations were performed using the sequence demarcation tool (sdt) version 1.2 in muscle mode []., using hts, we identified 21 parvovirus sequences in samples derived from rodents, bats, opossums, birds and cattle in pernambuco, são […]

PMCID: 5869529
PMID: 29562672
DOI: 10.3390/v10030136

[…] bootstrap replicates and the resulting trees were visualized in figtree (version 1.4.2) []. branches that had less than 50% bootstrap support were collapsed. sequence identity analysis using the sequence demarcation tool (sdt) (version 1.2) [] was carried out on the aligned amplicon clusters of each viral rna segment., full length genome sequences of the australian apmv isolate k75 and pdv […]

PMCID: 5869500
PMID: 29498637
DOI: 10.3390/v10030107

[…] primer walking. sequence contigs were assembled into full genomes using dna baser v4 (heracle biosoft s.r.l., pitesti, romania)., the genetic diversity among the gocv isolates was analyzed using sdt v1.2 []. given that recombination has been detected in a range of other circoviruses, prior to phylogenetic analysis the 63 gocv full genome sequences were aligned using muscle [] and analyzed […]


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SDT institution(s)
Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa

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