SplitsTree protocols

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SplitsTree specifications


Unique identifier OMICS_08887
Name SplitsTree
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Medium
Version 4.0
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/SplitsTree


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Publications for SplitsTree

SplitsTree in pipelines

PMCID: 5766536
PMID: 29330451
DOI: 10.1038/s41598-017-16399-x

[…] score below 0.95 (16/244 columns removed in the rt sequence from camv). the resulting msa was then used to build the sequence similarity network shown in fig.  and supplementary fig.  with splitstree4  applying the neighbornet method with uncorrected p distance model and 1,000 bootstrap tests. manual analysis of this network enabled the discrimination of 17 distinct groups sharing deep […]

PMCID: 5809883
PMID: 29433445
DOI: 10.1186/s12864-018-4531-2

[…] to estimate the best-fit substitution model. the genome of shewanella denitrificans os217 was chosen to serve as an outgroup. the phylogenetic network of the concatenated data was constructed using splitstree v4.14.6, with a neighbor net drawing and jukes-cantor correction []. a pan-genome tree was constructed according to the presence/absence of all homologous genes using raxml. besides, […]

PMCID: 5825158
PMID: 29432421
DOI: 10.1371/journal.pgen.1007155

[…] pegas, ape and adegenet packages in r [–] to manipulate and visualize the genetic distances of all samples as well as the hpg1 subset (supplementary text 7). we constructed parsimony networks using splitstree v.4.12.3 [], with confidence values calculated with 1,000 bootstrap iterations. we built maximum clade credibility trees using the bayesian phylogenetic tools implemented in beast v.1.8 [] […]

PMCID: 5860741
PMID: 29558470
DOI: 10.1371/journal.pone.0193718

[…] analyzed for gc content (mol %), gc % deviation from their respective genomes (table b in ) as well as p-distance calculations through mega 7.0. phylogenetic network analysis was performed using splitstree software [] (figures e and f in )., the genbank accession numbers for the 16s rrna, gyrb, atpg, dnaj, rpob, arsc, narg, and nirs gene sequences of strain kas 5-3t are jx173988, kx827793, […]

PMCID: 5947664
PMID: 29423949
DOI: 10.1111/tbed.12809

[…] with branch swapping by tree‐bisection‐reconnection. one hundred bootstrap replicates were conducted to assess statistical support for the tree topology. phylogenetic networks were constructed using splitstree v. 4 (huson & bryant, ), using the uncorrected p characters transformation. regions of potential recombination with ehv‐4 and ehv‐8 were also investigated by identifying individual […]

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SplitsTree in publications

PMCID: 5955891
PMID: 29769695
DOI: 10.1038/s41598-018-26073-5

[…] were obtained by dividing the pairwise mums’ sum by the average genome size of the two paired genomes (mumi genomic distance). bionj trees were generated from the mumi distance matrix using splitstree4. blast analysis was used to assess sequence identity between the blashv-12-surrounding region and nucleotide sequences deposited to ncbi., plasmid conjugation was assessed in solid mating […]

PMCID: 5934806
PMID: 29724185
DOI: 10.1186/s12879-018-3114-9

[…] and other virulence factors were examined using multiplex pcr. diversity was calculated using divein, clonal relationship was determined using eburst, and phylogenetic analysis was performed using splitstree4., a polyclonal oxa-48 gene alone was the most common carbapenemase detected in 48/71 (67.6%) isolates followed by ndm-1 alone in 9/71 (12.7%) isolates. coproduction of oxa-48 and ndm-1 […]

PMCID: 5930637
PMID: 29743928
DOI: 10.1186/s12983-018-0262-0

[…] no filter [, ]. this methodology decomposes all gene trees into quartets to build supernetworks where edge lengths correspond to quartet frequencies. resulting supernetworks were visualized in splitstree 4.14.6 []., dating analyses were calibrated using fossils relevant to the origin of dytiscoidea and geadephaga, elateriformia and scarabaeiformia [, , ]. the earliest fossils […]

PMCID: 5932162
PMID: 29755435
DOI: 10.3389/fmicb.2018.00806

[…] to account for the rate of heterogeneity among sites. the consensus tree was rooted with the “midpoint root” option in figtree, and nodes were arranged in increasing order. we built a neighbornet splitstree using the program splitstree4 () with default settings. based on the set of snp positions, isolates were also grouped together by a maximum distance of distinct snp positions […]

PMCID: 5936940
PMID: 29765675
DOI: 10.1098/rsos.172212

[…] (iz34), l. naiffi mdas/br/1979/m5533 (ioc_l1365) and l. lainsoni mhom/br/1981/m6426 (ioc_l1023). the genes were aligned using clustal omega v1.1 [] to create a network for the 102 isolates with splitstree v4.13.1 []. this replicated the expected highly reticulated structure [], where l. braziliensis m2904 and l. peruviana pab-4377 were in the l. braziliensis cluster (). figure 1., previous […]

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SplitsTree institution(s)
Center for Bioinformatics ZBIT, Tübingen University, Tübingen, Germany

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