Tag: DISTANCE

GGDC 3.0 – Genome-to-Genome Distance Calculator

GGDC 3.0

:: DESCRIPTION

GGDC  is an updated and enhanced version with improved DDH-prediction models and additional features such as confidence-interval estimation. To the best of our knowledge, it is the only digital DDH method that provides this feature. Of all genome-based methods we are aware of, GGDC 2.0 yields the highest correspondence to wet-lab DDH (without sharing DDH’s drawbacks).

::DEVELOPER

Leibniz Institute DSMZ

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Feb 21;14:60. doi: 10.1186/1471-2105-14-60.
Genome sequence-based species delimitation with confidence intervals and improved distance functions.
Meier-Kolthoff JP1, Auch AF, Klenk HP, Göker M.

LocalDiff 201309 – Characterize Non-stationary Patterns of Isolation by Distance

LocalDiff 201309

:: DESCRIPTION

LocalDiff provides Bayesian measures of Local Genetic Differentiation to characterize non-stationary patterns of isolation by distance.

::DEVELOPER

Nicolas Duforet-Frebourg and Michael Blum

:: SCREENSHOTS

LocalDiff

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 LocalDiff

:: MORE INFORMATION

Citation

Non-stationary patterns of isolation-by-distance: inferring measures of genetic Friction.
Nicolas Duforet-Frebourg, Michael G. B. Blum.
arXiv:1209.5242

DistanceSVM – Using Distances between Top-n-gram and Residue Pairs for Protein remote Homology Detection

DistanceSVM

:: DESCRIPTION

DistanceSVM is the method of Using distances between Top-n-gram and residue pairs for protein remote homology detection.

::DEVELOPER

Bin Liu’s lab,

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Windows
  • PSI-BLAST package

:: DOWNLOAD

 DistanceSVM

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014;15 Suppl 2:S3. doi: 10.1186/1471-2105-15-S2-S3. Epub 2014 Jan 24.
Using distances between Top-n-gram and residue pairs for protein remote homology detection.
Liu B, Xu J, Zou Q, Xu R, Wang X, Chen Q.

ALFRED-G – Distance Estimator for Phylogenetic Inference

ALFRED-G

:: DESCRIPTION

ALFRED-G is an Alignment Free Distance Estimator software for Phylogenetic Inference. It takes as input a set of n sequences and ouputs an n x n matrix of distance estimate for use in Phylogenetic inference.

::DEVELOPER

Prof. Srinivas Aluru Research group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ALFRED-G

:: MORE INFORMATION

Citation

Thankachan SV, Chockalingam SP, Liu Y, Krishnan A, Aluru S.
A greedy alignment-free distance estimator for phylogenetic inference.
BMC Bioinformatics. 2017 Jun 7;18(Suppl 8):238. doi: 10.1186/s12859-017-1658-0. PMID: 28617225; PMCID: PMC5471951.

MODICOS 2.4.1 – Morphometric and Distance Computation Software

MODICOS 2.4.1

:: DESCRIPTION

MODICOS allows to compute euclidean distances and centroid size (CS) from a set of coordinates x,y and use CS to estimate heritabilities and Qst. It also computes relative warps and uniform components of shape variation from a set of coordinates x,y and use any relative warp or uniform component to estimate heritabilities and Qst’s.

::DEVELOPER

Antonio Carvajal-Rodriguez 

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  MODICOS

:: MORE INFORMATION

Citation

Carvajal-Rodríguez A, Rodríguez MG 2005.
Morphometric and Distance Computation Software oriented for evolutionary studies.
Online Journal of Bioinformatics 6 : 34-41.

NucType 1.5 – Measure Distances/Size of Chromosomes and analysis Karyotype

NucType 1.5

:: DESCRIPTION

NucType is tool to measure distances/size of chromosomes, group the chromosomes and analysis the karyotype (karyotype asymmetry indices). Additionally it has a tool to measure the pollen or leaves.

::DEVELOPER

Yan Yu

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  NucType

:: MORE INFORMATION

DTscore – Fast and Accurate Distance Algorithm to Reconstruct Tandem Duplication Trees

DTscore

:: DESCRIPTION

DTscore is a distance based tamdem duplication tree reconstruction algorithm. It is based on a simple tandem duplication model, which assumes unequal recombination (crossover) as the only duplication mechanism. All it takes as input is a distance matrix between copies. In this matrix, the rows and columns need to be ordered in the same way as the copies are ordered on the locus. DTscore can be applied to relatively large datasets (more than a hundred copies). Distances can be calculated using programs such as DNADIST (nucleotide sequences) or PROTDIST (protein sequences) from the PHYLIP package. Heterogeneous rates of substitution among sites can be dealt with using the GAMMA method, for example.

::DEVELOPER

DTscore team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 DTscore

:: MORE INFORMATION

Citation

Elemento O. and Gascuel O.
An efficient and accurate distance based algorithm to reconstruct tandem duplication trees.
Bioinformatics. 2002 18 :S92-S99.

EMDomics 2.22.0 – Earth Mover’s Distance for Differential Analysis of Genomics Data

EMDomics 2.22.0

:: DESCRIPTION

The EMDomics algorithm is used to perform a supervised multi-class analysis to measure the magnitude and statistical significance of observed continuous genomics data between groups.

::DEVELOPER

Beck Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 EMDomics

:: MORE INFORMATION

Citation

EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes.
Nabavi S, Schmolze D, Maitituoheti M, Malladi S, Beck AH.
Bioinformatics. 2015 Oct 29. pii: btv634.

MIDER v2 – Mutual Information Distance and Entropy Reduction

MIDER v2

:: DESCRIPTION

MIDER is a general purpose software tool for inferring network structures. It has been developed with biological networks in mind, but can be applied in other areas.

::DEVELOPER

(Bio)Process Engineering group, IIM-CSIC

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux /Windows/MacOsX
  • MatLab

:: DOWNLOAD

 MIDER

:: MORE INFORMATION

Citation

MIDER: Network Inference with Mutual Information Distance and Entropy Reduction.
Villaverde AF, Ross J, Morán F, Banga JR.
PLoS One. 2014 May 7;9(5):e96732. doi: 10.1371/journal.pone.0096732. eCollection 2014.

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