HypoTrace – Image Analysis Software for Measuring Hypocotyl Growth and Shape

HypoTrace

:: DESCRIPTION

HypoTrace takes time series of image files as input and output growth rate as well as hook angle measurements for Hypocotyls. The software comes with a build-in Graphical User Interface, which allows the software to be run under three modes: 1. Automatic mode with no user intervention, good for high quality images; 2. Semi-Auto mode with a little bit user intervention, good for fair quality images; 3. Manual mode, work for all images including really bad quality images. The three modes are designed to effectively detect the cotyledons bifurcation point under all conditions.

::DEVELOPER

Liya Wang

:: SCREENSHOTS

HypoTrace

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Matlab

:: DOWNLOAD

 HypoTrace

:: MORE INFORMATION

Citation

Wang L., Uilecan I. V., Assadi A. H., Kozmik C. A., Spalding E. P.,
HypoTrace: Image Analysis Software for Measuring Hypocotyl Growth and Shape Demonstrated on Arabidopsis Seedlings Undergoing Photomorphogenesis,
Plant Physiol. 2009, 149(4), 1632-1637.

QCC 1.1 – Measure Reproducibility of ChIP-chip data

 QCC 1.1

:: DESCRIPTION

QCC  (Quantized correlation coefficient) is an  R package computes a robust measurement of the reproducibility of ChIP-chip data.The QCC statistic can also be applied in a variety of other contexts for measuring reproducibility, including analysis of array CGH data for DNA copy number and gene expression data.

::DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 QCC

:: MORE INFORMATION

Citation

Peng S, Kuroda MI, Park PJ.
Quantized correlation coefficient for measuring reproducibility of ChIP-chip data
BMC Bioinformatics. 2010; 11: 399.

Repeat Enrichment Estimator – Measure Enrichment of Annotated Repeat Types in ChIP-seq data

Repeat Enrichment Estimator

:: DESCRIPTION

Repeat enrichment estimator aims to measure the enrichment of annotated repeat types in ChIP-seq data

::DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  Repeat enrichment estimator

:: MORE INFORMATION

Citation

Daniel S Day, Lovelace J Luquette, Peter J Park and Peter V Kharchenko.
Estimating enrichment of repetitive elements from high-throughput sequence data.
Genome Biology 2010, 11:R69 doi:10.1186/gb-2010-11-6-r69

Selfish – Discovery of Differential Chromatin Interactions via a Self-Similarity Measure

Selfish

:: DESCRIPTION

SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps. It uses self-similarity to model interactions in a robust way.

::DEVELOPER

Lonardi Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Matlab

:: DOWNLOAD

SELFISH

:: MORE INFORMATION

Citation

Ardakany AR, Ay F, Lonardi S.
Selfish: discovery of differential chromatin interactions via a self-similarity measure.
Bioinformatics. 2019 Jul 15;35(14):i145-i153. doi: 10.1093/bioinformatics/btz362. PMID: 31510653; PMCID: PMC6612869.

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

NucType

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  NucType

:: MORE INFORMATION

BaTS 1.0 – Measure and Test Phylogeny Trait Associations

BaTS 1.0

:: DESCRIPTION

BaTS (Bayesian Tip-Significance testing) is a package that allows the user to test for significant phylogeny-trait correlations whilst taking into account uncertainty arising from phylogenetic error, by integrating over the credible set of topologies produced by Bayesian phylogenetics programs such as BEAST or MrBayes. Null distributions are generated for statistics of phylogeny-trait association, and used to test the significance of the observed data. BaTS can also perform batch analyses of multiple data sets.

::DEVELOPER

Joe Parker

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Java

:: DOWNLOAD

BaTS

:: MORE INFORMATION

Citation:

Parker J, Rambaut A, Pybus OG. 2008.
Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty.
Infection, Genetics and Evolution 8:239-46

FastSemSim 1.0 – Semantic Similarity Measures

FastSemSim 1.0

:: DESCRIPTION

FastSemSim is a package that implements several semantic similarity measures. It is both a library and an end-user application, featuring an intuitive graphical user interface (GUI). It has been implemented with the aim of being fast, expandable, and easy to use. It allows the user to work with the most updated version of GO database and customizable annotation corpora. It provides a set of logically-organized classes that can be easily exploited to both integrate semantic similarity into different analysis pipelines and extend the library with new measures.

::DEVELOPER

Marco Mina

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 FastSemSim

:: MORE INFORMATION

JSpecies 1.2.1 / JSpeciesWS – Measure the Probability if two Genomes belonging to the Same Species

JSpecies 1.2.1 / JSpeciesWS

:: DESCRIPTION

JSpecies is an easy to use, biologist-centric software designed to measure the probability if two genomes belonging to the same species or not.

JSpeciesWS is a quick and easy to use online service to measure the probability if two or more (draft) genomes belong to the same species or not by pairwise comparison of (1) their Average Nucleotide Identity (ANI) and/or (2) correlation indexes of their Tetra-nucleotide signatures

::DEVELOPER

JSpecies Team

:: SCREENSHOTS

JSpecies

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • Java

:: DOWNLOAD

 JSpecies ,JSpeciesWS

:: MORE INFORMATION

Citation

Richter M, & Rosselló-Móra R (2009)
Shifting the genomic gold standard for the prokaryotic species definition.
Proc Natl Acad Sci USA 106(45):19126-31.

JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison.
Richter M, Rosselló-Móra R, Glöckner FO, Peplies J.
Bioinformatics. 2015 Nov 16. pii: btv681

infocalc 1.1 – Measure the Ancestry Information Content of Genetic Markers

infocalc 1.1

:: DESCRIPTION

infocalc is a small script for calculating statistics that measure the ancestry information content of genetic markers.

::DEVELOPER

Rosenberg lab at Stanford University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Perl

:: DOWNLOAD

  infocalc

:: MORE INFORMATION

Citation

Informativeness of genetic markers for inference of ancestry.
Rosenberg NA, Li LM, Ward R, Pritchard JK.
Am J Hum Genet. 2003 Dec;73(6):1402-22. Epub 2003 Nov 20.

simDEF – Definition-based Semantic Similarity Measure of GO Terms for Functional Similarity Analysis of Genes

simDEF

:: DESCRIPTION

simDEF is an efficient method for measuring semantic similarity of GO terms using their GO definitions.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

  simDEF

:: MORE INFORMATION

Citation:

simDEF: Definition-based Semantic Similarity Measure of Gene Ontology Terms for Functional Similarity Analysis of Genes.
Pesaranghader A, Matwin S, Sokolova M, Beiko RG.
Bioinformatics. 2015 Dec 26. pii: btv755.