Tag: Partitioning

LSA – Metagenomic Read Partitioning by Latent Factor analysis

LSA

:: DESCRIPTION

LSA (Latent Strain Analysis) partitions reads into sets likely belonging to the same genome, using the covariance of k-mers across many samples.

::DEVELOPER

The Alm lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux
  • Python

:: DOWNLOAD

LSA

:: MORE INFORMATION

Citation

Cleary B, Brito IL, Huang K, Gevers D, Shea T, Young S, Alm EJ.
Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning.
Nat Biotechnol. 2015 Oct;33(10):1053-60. doi: 10.1038/nbt.3329. Epub 2015 Sep 14. PMID: 26368049; PMCID: PMC4720164.

AdaptML 1.0 – Partitioning of Gene Sequences according to their Genetic and Ecological Similarity

AdaptML 1.0

:: DESCRIPTION

AdaptML is a software package that will automatically partition groups of gene sequences according to both their genetic and ecological similarity.

::DEVELOPER

The Alm lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Python

:: DOWNLOAD

 AdaptML

:: MORE INFORMATION

Citation

Science. 2008 May 23;320(5879):1081-5. doi: 10.1126/science.1157890.
Resource partitioning and sympatric differentiation among closely related bacterioplankton.
Hunt DE, David LA, Gevers D, Preheim SP, Alm EJ, Polz MF.

CellAging – Study Segregation and Partitioning in Division in Cell Lineages of Escherichia coli

CellAging

:: DESCRIPTION

CellAging is a tool designed to automatically extract information on the segregation of aggregates to the cell poles and their partitioning in division and on cellular vitality from temporal images of E. coli cells, obtained by parallel brightfield and fluorescence microscopy.

::DEVELOPER

Andre Ribeiro’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • MatLab

:: DOWNLOAD

 CellAging

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):1708-9. doi: 10.1093/bioinformatics/btt194. Epub 2013 Apr 23.
CellAging: a tool to study segregation and partitioning in division in cell lineages of Escherichia coli.
Antti Hakkinen, Muthukrishnan AB, Mora A, Fonseca JM, Ribeiro AS.

HTJoinSolver 0.4A – Human Immunoglobulin VDJ Partitioning

HTJoinSolver 0.4A

:: DESCRIPTION

HTJoinSolver is a pubically available application to assist researchers in partitioning the V(D)J regions of immunogloblulin.

::DEVELOPER

the Office of Intramural Research, Center for Information Technology in collaboration with the Vaccine Research Center at the National Institute of Allergy and Infectious Diseases.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • JRE

:: DOWNLOAD

 HTJoinSolver

:: MORE INFORMATION

Citation

HTJoinSolver: Human immunoglobulin VDJ partitioning using approximate dynamic programming constrained by conserved motifs.
Russ DE, Ho KY, Longo NS.
BMC Bioinformatics. 2015 May 23;16(1):170. doi: 10.1186/s12859-015-0589-x.

TriageTools 0.2.2 – Partitioning and Prioritizing Fastq data

TriageTools 0.2.2

:: DESCRIPTION

TriageTools is a collection of tools for partitioning raw data (fastq reads) from high-throughput sequencing projects.

::DEVELOPER

TriageTools team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 TriageTools

:: MORE INFORMATION

Citation

TriageTools: tools for partitioning and prioritizing analysis of high-throughput sequencing data.
Fimereli D, Detours V, Konopka T.
Nucleic Acids Res. 2013 Apr;41(7):e86. doi: 10.1093/nar/gkt094

clusterGenomics 1.0 – Identifying Clusters in Genomics data by recursive Partitioning

clusterGenomics 1.0

:: DESCRIPTION

clusterGenomics is an R package of identifying clusters in genomics data by recursive partitioning

::DEVELOPER

Research Group for Biomedical Informatics (BMI)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

 clusterGenomics

:: MORE INFORMATION

Citation:

Stat Appl Genet Mol Biol. 2013 Oct 1;12(5):637-52. doi: 10.1515/sagmb-2013-0016.
Identifying clusters in genomics data by recursive partitioning.
Nilsen G, Borgan O, Liestøl K, Lingjærde OC.

GPMAP – Global Haplotype Partitioning for Maximal Associated SNP Pairs

GPMAP

:: DESCRIPTION

GPMAP has been developed based on the open source code of Haploview (ver. 4.1). Therefore GPMAP basically inherits all Haploview functions plus the global partitioning method

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • Java

:: DOWNLOAD

GPMAP

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Aug 27;10:269. doi: 10.1186/1471-2105-10-269.
Global haplotype partitioning for maximal associated SNP pairs.
Katanforoush A1, Sadeghi M, Pezeshk H, Elahi E.

Exit mobile version