Tag: RAP

RAP / RAP-Green – Phylogenetic Tree Reconciler

RAP / RapGreen

:: DESCRIPTION

RAP is an algorithm and a software have been developed, which permit to find gene duplications in phylogenetic trees, in order to improve gene function inferences. The algorithm is applicable to realistic data, especially n-ary species tree and unrooted phylogenetic tree

RAP-Green is a new implementation and an improvment of the RAP software which permits to compare gene and species trees, infers duplication events, and provide confidence score in function conservation between genes.

::DEVELOPER

South Green bioinformatics platform

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /  Mac OsX / Windows
  • Java

:: DOWNLOAD

  RAP , RapGreen

:: MORE INFORMATION

Citation

Dufayard JF, Bocs S, Guignon V, Larivière D, Louis A, Oubda N, Rouard M, Ruiz M, de Lamotte F.
RapGreen, an interactive software and web package to explore and analyze phylogenetic trees.
NAR Genom Bioinform. 2021 Sep 23;3(3):lqab088. doi: 10.1093/nargab/lqab088. PMID: 34568824; PMCID: PMC8459725.

RAP – Rank Aggregation-based data Fusion for Gene Prioritization

RAP

:: DESCRIPTION

RAP is a rank aggregation-based data fusion approach for gene prioritization in plants. It can be used to perform the gene prioritization in Arabidopsis thaliana and 28 non-plant species.

::DEVELOPER

Ma Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

RAP

:: MORE INFORMATION

Citation

Zhai J, Tang Y, Yuan H, Wang L, Shang H, Ma C.
A Meta-Analysis Based Method for Prioritizing Candidate Genes Involved in a Pre-specific Function.
Front Plant Sci. 2016 Dec 15;7:1914. doi: 10.3389/fpls.2016.01914. PMID: 28018423; PMCID: PMC5156684.

RAP – Association Analysis Approach to Biclustering

RAP

:: DESCRIPTION

RAP (Range-support Association Pattern) is an novel approach based on association pattern analysis for discovering constant-row biclusters in gene expression data. Contrary to traditional association pattern discovery approaches, RAP works with real valued data sets without discritizing them. RAP discovers small highly coherent biclusters as opposed to large blocks discovered by traditional biclustering approaches.

::DEVELOPER

Data mining for biomedical informatics at the UMN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 RAP

:: MORE INFORMATION

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