DupLoCut – Duplication Loss Phylogeny by Cutting Planes

DupLoCut

:: DESCRIPTION

DupLoCut computes ancestral gene orders, given a phylogenetic tree and gene orders assigned to the leaves of the tree. It attempts to find the most parsimony assignment of gene orders under the duplication-loss evolutionary model.

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

  DupLoCut

:: MORE INFORMATION

Citation

J Comput Biol. 2013 Sep;20(9):643-59. doi: 10.1089/cmb.2013.0057.
The duplication-loss small phylogeny problem: from cherries to trees.
Andreotti S1, Reinert K, Canzar S.

CLImAT 1.2.2 – Detection of Copy Number Alteration and Loss of Heterozygosity

CLImAT 1.2.2

:: DESCRIPTION

CLImAT (CNA and LOH Assessment in Impure and Aneuploid Tumors) is a bioinformatic tool for identification of genome-wide aberrations from tumor samples using whole-genome sequencing data.

::DEVELOPER

HI_Lab @ USTC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/MacOsX/Linux
  • Matlab

:: DOWNLOAD

 CLImAT

:: MORE INFORMATION

Citation:

CLImAT: accurate detection of copy number alteration and loss of heterozygosity in impure and aneuploid tumor samples using whole-genome sequencing data.
Yu Z, Liu Y, Shen Y, Wang M, Li A.
Bioinformatics. 2014 Sep 15;30(18):2576-83. doi: 10.1093/bioinformatics/btu346.

DynaDup 2.3.2 – Inferring Optimal Species Trees under Gene Duplication and Loss

DynaDup 2.3.2

:: DESCRIPTION

DynaDup is a Dynamic Programing based Java application for building species trees from gene trees minimizing gene duplication and gene duplication and loss.

::DEVELOPER

The Warnow Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows/MacOsX
  • Java

:: DOWNLOAD

 DynaDup

:: MORE INFORMATION

Citation

Pac Symp Biocomput. 2013:250-61.
Inferring optimal species trees under gene duplication and loss.
Bayzid MS1, Mirarab S, Warnow T.

hapLOH 14 – Analysis of loss of Heterozygosity in Tumor Genomes

hapLOH 1.4

:: DESCRIPTION

hapLOH profiles and characterizes tumor genomes using data from SNP microarrays. It is designed to be effective in the presence of high levels of germline contamination.

::DEVELOPER

paul scheet lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Perl
  • Python

:: DOWNLOAD

  hapLOH

:: MORE INFORMATION

Citation

Vattathil, Selina, and Paul Scheet.
Haplotype-based profiling of subtle allelic imbalance with SNP arrays.
Genome research 23.1 (2013): 152-158.

GISTIC 2.0.22 – Detect Regions of Significant Copy-number Gains and Losses

GISTIC 2.0.22

:: DESCRIPTION

GISTIC  (Genomic Identification of Significant Targets in Cancer) facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

::DEVELOPER

The Cancer Genome Analysis (CGA) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GISTIC

:: MORE INFORMATION

Citation

Genome Biol. 2011;12(4):R41. Epub 2011 Apr 28.
GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers.
Mermel CH, Schumacher SE, Hill B, Meyerson ML, Beroukhim R, Getz G.

GLOOME 201305 – Gain Loss Mapping Engine

GLOOME 201305

:: DESCRIPTION

The main purpose of GLOOME server is to accurately infers branch specific and site specific gain and loss events.

:: DEVELOPER

Edmond J. Safra Center for Bioinformatics  at Tel-Aviv university.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GLOOME

:: MORE INFORMATION

Citation:

Genome Biol Evol. 2011;3:1265-75. doi: 10.1093/gbe/evr101. Epub 2011 Oct 4.
Inference of gain and loss events from phyletic patterns using stochastic mapping and maximum parsimony–a simulation study.
Cohen O1, Pupko T.

GLOOME: gain loss mapping engine.
Cohen O, Ashkenazy H, Belinky F, Huchon D, Pupko T.
Bioinformatics. 2010 Nov 15;26(22):2914-5. doi: 10.1093/bioinformatics/btq549.

ExomeCNV 1.4 – Exome Sequencing-based Copy-number Variation and Loss of Heterozygosity Detection

ExomeCNV 1.4

:: DESCRIPTION

ExomeCNV, a statistical method to detect CNV and LOH using depth-of-coverage and B-allele frequencies, from mapped short sequence reads.

::DEVELOPER

Nelsonlab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R package
  • Perl
  • Python
  • Samtool
  • GATK

:: DOWNLOAD

 ExomeCNV

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Oct 1;27(19):2648-54. doi: 10.1093/bioinformatics/btr462. Epub 2011 Aug 9.
Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV.
Sathirapongsasuti JF, Lee H, Horst BA, Brunner G, Cochran AJ, Binder S, Quackenbush J, Nelson SF.

Ultrasome 1.0 – Detect Gains and Losses of Chromosomal Material in DNA copy-number data

Ultrasome 1.0

:: DESCRIPTION

Ultrasome is an extremely efficient methodology for detecting gains and losses of chromosomal material in DNA copy-number data. The program processes latest-generation copy number arrays about 10,000 times faster than standard methods (e.g., CBS) while retaining comparable analyticaccuracy.

::DEVELOPER

The Broad Institute, Cambridge, MA

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 Ultrasome

:: MORE INFORMATION

Citation

Björn Nilsson et al.
Ultrasome: efficient aberration caller for copy numberstudies of ultra-high resolution
Bioinformatics (2009) 25 (8): 1078-1079.
http://bioinformatics.oxfordjournals.org/content/25/8/1078.abstract