primetv specifications

Information


Unique identifier OMICS_10473
Name primetv
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.5.6
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Bengt Sennblad <>

Information


Unique identifier OMICS_10473
Name primetv
Interface Web user interface
Restrictions to use None
Programming languages C++
Computer skills Basic
Version 1.5.6
Stability Stable
Maintained Yes

Maintainer


  • person_outline Bengt Sennblad <>

Publication for primetv

primetv in publications

 (3)
PMCID: 5381371
PMID: 25339375
DOI: 10.1038/srep06746

[…] trees were sampled every 1000th iteration over 1.1 million generations after a burn-in of 101 samples., the reconciled trees were built using most parsimonious reconciliations methods and viewed by primetv. the species tree was built based on the alpha tubulin gene tree and manually edited according to the previous studies., the codeml program from the paml 4.7 package was used to estimate […]

PMCID: 4057122
PMID: 24926798
DOI: 10.1371/journal.pone.0099673

[…] most parsimonious reconciliation of the estimated gene tree and the species tree was performed with notung 2.6 , and represented with figtree v1.3.1 (http://tree.bio.ed.ac.uk/software/figtree/) and primetv . synteny was investigated with genomicus v69.01 ., fish care and challenge experiments were conducted according the csic national committee on bioethics guidelines under approval number id […]

PMCID: 3433342
PMID: 22697058
DOI: 10.1186/1471-2148-12-86

[…] using all snps of non-p/a genes among genomes, based on the neighbor-joining method []. a reconciled tree, which was viewed as the evolved p/a tree in the accession tree, was then illustrated using primetv software []., we built a local database of all col genes, and then every gene was subjected to the blastn search to identify homologous genes. a criterion of ≥70% nucleotide identity was used […]


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primetv institution(s)
Stockholm Bioinformatics Center and Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden; Stockholm Bioinformatics Center and School of Computer Science and Communication, KTH, Stockholm, Sweden

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