Barnacle 1.0.3 – Detecting and Characterizing Tandem Duplications and Fusions in Transcriptome Assembly

Barnacle 1.0.3

:: DESCRIPTION

Barnacle (Browsing Assembled RNA for Chimeras with Localized Evidence) is a pipeline for detecting and characterizing chimeric transcripts from long RNA sequences, such as those generated by de novo transcriptome assembly.

::DEVELOPER

Canada’s Michael Smith Genome Sciences Centre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Barnacle

:: MORE INFORMATION

Citation

BMC Genomics. 2013 Aug 14;14:550. doi: 10.1186/1471-2164-14-550.
Barnacle: detecting and characterizing tandem duplications and fusions in transcriptome assemblies.
Swanson L et al.

PolytomySolverNAD 0.1 – Polytomy Refinement for the Correction of Dubious Duplications in Gene Trees

PolytomySolverNAD 0.1

:: DESCRIPTION

Given a rooted binary gene tree and species tree, PolytomySolverNAD corrects a NAD (Non-Apparent Duplication) of the gene tree by applying multifurcation.

::DEVELOPER

MANUEL LAFOND

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

  PolytomySolverNAD

:: MORE INFORMATION

Citation

Polytomy refinement for the correction of dubious duplications in gene trees.
Lafond M, Chauve C, Dondi R, El-Mabrouk N.
Bioinformatics. 2014 Sep 1;30(17):i519-i526. doi: 10.1093/bioinformatics/btu463.

CNViewer 20111128 – Identification of Duplications, Insertions or LOH that Segregates with a Disease Phenotype

CNViewer 20111128

:: DESCRIPTION

CNViewer aids the identification of regions of abnormal copy number variation that segregates with a disease phenotype in small pedigree.

::DEVELOPER

Leeds Institute of Molecular Medicine

:: SCREENSHOTS

CNViewer1

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0 

:: DOWNLOAD

 CNViewer

:: MORE INFORMATION

Citation

PLoS One. 2012;7(8):e43466. doi: 10.1371/journal.pone.0043466. Epub 2012 Aug 17.
Rapid visualisation of microarray copy number data for the detection of structural variations linked to a disease phenotype.
Carr IM, Diggle CP, Khan K, Inglehearn C, McKibbin M, Bonthron DT, Markham AF, Anwar R, Dobbie A, Pena SD, Ali M.

LcaMap – Simultaneous Identification of Duplications, Losses and Lateral Gene Transfers

LcaMap

:: DESCRIPTION

LcaMap is a software for simultaneous identification of duplication, losses and lateral gene transfers. LcaMap takes a gene tree G, a species tree S, and the costs of a lateral gene transfer, a gene duplication, and a gene loss as its input. It outputs all minimum-cost LCA-reconciliations between G and S.

::DEVELOPER

Lusheng Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 LcaMap

:: MORE INFORMATION