Tag: Infer

iGTP 1.1 – Infer Species Phylogenies from Gene Phylogenies

iGTP 1.1

:: DESCRIPTION

iGTP is a program designed to help biologists infer species phylogenies from gene phylogenies, using the gene tree parsimony (GTP) approach. The program implements efficient heuristics which allows it to handle large-scale species tree inference under the duplication, duplication-loss, and deep coalescence reconciliation costs.

::DEVELOPER

Computational Biology Laboratory, Department of Computer Science,Iowa State University

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 iGTP

:: MORE INFORMATION

Citation

Ruchi Chaudhary, Mukul S. Bansal, André Wehe, David Fernández-Baca, Oliver Eulenstein,
“iGTP: A software package for large-scale gene tree parsimony analysis“,
BMC Bioinformatics 2010, 11:574.

IMIG – Infer Recent Migration rates from Individual Genotypes

IMIG

:: DESCRIPTION

IMIG (Inferring recent Migration rates from Individual Genotypes) aims at estimating pairwise rates of migration between discrete populations using multilocus genotypes.

::DEVELOPER

Thomas Broquet (thomas.broquet@unil.ch) and Jon Yearsley (jon.yearsley@ucd.ie)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 IMIG

:: MORE INFORMATION

Citation

Mol Ecol. 2009 Mar;18(6):1048-60. Epub 2009 Feb 9.
Inferring recent migration rates from individual genotypes.
Broquet T, Yearsley J, Hirzel AH, Goudet J, Perrin N.

TREESELECT 1.1 – Infer Natural Selection from unusual Population Differentiation

TREESELECT 1.1

:: DESCRIPTION

TreeSelect is a software package for inferring natural selection from unusual population differentiation between closely related populations.

::DEVELOPER

Alkes Price

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 TreeSelect

:: MORE INFORMATION

Citation:

Bhatia et al. (2011),
“Genome-wide comparison of African-ancestry populations from CARe and other cohorts reveals signals of natural selection“,
American Journal of Human Genetics, 89(3):368-381.

Parente 2.0.1 – Infer Relatedness (IBD) between pairs of Related Individuals

Parente 2.0.1

:: DESCRIPTION

Parente is a method for detecting relatedness. It detects IBD accurately and rapidly using an embedded likelihood ratio test.

::DEVELOPER

Serafim’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Parente

:: MORE INFORMATION

Citation

An Accurate Method for Inferring Relatedness in Large Datasets of Unphased Genotypes via an Embeddeded Likelihood-Ratio Test.
Jesse M. Rodriguez, Serafim Batzoglou, Sivan Bercovici.
Research in Computational Molecular Biology , Lecture Notes in Computer Science Volume 7821, 2013, pp 212-229

Cancerin – Infer Competing Endogenous RNA (ceRNA) interactions in Cancer

Cancerin

:: DESCRIPTION

Cancerin is a tool to infer genome-wide cancer-associated ceRNA interaction network in cancer.

::DEVELOPER

Bozdag Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

Cancerin

:: MORE INFORMATION

Citation

Do D, Bozdag S.
Cancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks.
PLoS Comput Biol. 2018 Jul 16;14(7):e1006318. doi: 10.1371/journal.pcbi.1006318. PMID: 30011266; PMCID: PMC6072113.

PyClone 0.13.1 – Infer Clonal Frequency Estimates of a Panel of deeply Sequenced Mutations

PyClone 0.13.1

:: DESCRIPTION

 pyClone is a software used to infer clonal frequency estimates of a panel of deeply sequenced mutations. The software is a Bayesian hierachical model for inferring the frequency of cells with a given mutation from allelic count data generated by next generation sequencing experiments. PyClone makes use of prior information about genotype as well as jointly analysing all mutations in a sample.

postpy is a set of tools to help with post-processing PyClone results.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

 PyClone, postpy

:: MORE INFORMATION

Citation

Sohrab P. Shah et al.
“The clonal and mutational evolution spectrum of primary triple-negative breast cancers”.
Nature 486, 395–399 (21 June 2012)
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DeterminePPI 1.0 – Inferring Protein-protein Interactions by Parsimony Principle

DeterminePPI 1.0

:: DESCRIPTION

DeterminePPI aims to infer protein-protein interaction by parsimony principle. Specifically, inferring domain interactions is formulated as an integer linear programming and solved by relaxed linear programming. In contrast to probabilistic algorithms, DeterminePPI is an algorithm based on a deterministic model.

::DEVELOPER

APORC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  DeterminePPI

:: MORE INFORMATION

Citation

Chen C, Zhao JF, Huang Q, Wang RS, Zhang XS.
Inferring domain-domain interactions from protein-protein interactions in the complex network conformation.
BMC Syst Biol. 2012;6 Suppl 1:S7. doi: 10.1186/1752-0509-6-S1-S7.

TargetScore 1.24.0 – Infer microRNA Targets using microRNA-overexpression data and Sequence Information

TargetScore 1.24.0

:: DESCRIPTION

TargetScore: a probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information

::DEVELOPER

Yue Li @ The Zhang Lab, University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Weindows/Linux/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 TargetScore

 :: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 1;30(5):621-8. doi: 10.1093/bioinformatics/btt599. Epub 2013 Oct 17.
A probabilistic approach to explore human miRNA targetome by integrating miRNA-overexpression data and sequence information.
Li Y1, Goldenberg A, Wong KC, Zhang Z.

PEER 1.3 – Infer Hidden Determinants and their effects from Gene Expression Profiles

PEER 1.3

:: DESCRIPTION

PEER is a collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods.

::DEVELOPER

Stegle group

:: REQUIREMENTS

:: DOWNLOAD

 PEER

:: MORE INFORMATION

Citation

Stegle O, Parts L, Durbin R, Winn J.
A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies.
PLoS Comput Biol. 2010 May 6;6(5):e1000770. doi: 10.1371/journal.pcbi.1000770.

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses.
Stegle O, Parts L, Piipari M, Winn J, Durbin R.
Nat Protoc. 2012 Feb 16;7(3):500-7. doi: 10.1038/nprot.2011.457.

AntigenicTreeTools 1.0 – Infer Antigenic Trees to resolve the Antigenic Impact of Amino Acid Changes

AntigenicTreeTools 1.0

:: DESCRIPTION

AntigenicTreeTools infer antigenic trees to resolve the antigenic impact of amino acid changes mapped to individual branches of a phylogenetic tree. For sufficiently resolved branches, this allows to quantify the antigenic impact of single amino acid changes. However, the software is also applicable to problems where a phylogenetic tree and pair-wise phenotypic distances are available.

::DEVELOPER

Algorithmic Bioinformatics, Heinrich-Heine-Universität Düsseldorf

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 AntigenicTreeTools

:: MORE INFORMATION

Citation:

Steinbrück L, McHardy AC (2012)
Inference of Genotype–Phenotype Relationships in the Antigenic Evolution of Human Influenza A (H3N2) Viruses.
PLoS Comput Biol 8(4): e1002492. doi:10.1371/journal.pcbi.1002492