RootAnnotator 201402 – Computes Root Posterior Probabilities given a sample of Rooted Trees

RootAnnotator 201402

:: DESCRIPTION

RootAnnotator computes root posterior probabilities. For this, it makes use of posterior collections of trees generated under clock models (e.g. .nexus files such as those generated by BEAST or MrBayes), from which branches wearing the root are identified and counted.

::DEVELOPER

RootAnnotator team

: SCREENSHOTS

RootAnnotator

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python
  • Java

:: DOWNLOAD

 RootAnnotator

:: MORE INFORMATION

Citation

Clock Rooting Further Demonstrates that Guinea 2014 EBOV is a Member of the Zaïre Lineage.
Calvignac-Spencer S, Schulze JM, Zickmann F, Renard BY.
PLoS Curr. 2014 Jun 16;6.

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

FamSeq 1.0.3 – Calculating Probability of Variants in Family-based Sequencing data

FamSeq 1.0.3

:: DESCRIPTION

FamSeq (Family-Based Sequencing) is a computational tool for calculating probability of variants in family-based sequencing data.

::DEVELOPER

Statistical Bioinformatics Lab, The University of Texas M. D. Anderson Cancer Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX/Windows
  • C++ Compiler

:: DOWNLOAD

   FamSeq

:: MORE INFORMATION

Citation

Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):3985-90. doi: 10.1073/pnas.1222158110.
Rare variant detection using family-based sequencing analysis.
Peng G, Fan Y, Palculict TB, Shen P, Ruteshouser EC, Chi AK, Davis RW, Huff V, Scharfe C, Wang W.

RASPberry 20141128 – Recombination via Ancestry Switch Probability

RASPberry 20141128

:: DESCRIPTION

RASPberry is a software for recombination rate inference using ancestry switch points in admixed individuals.

::DEVELOPER

Novembre Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 RASPberry

 :: MORE INFORMATION

Citation

 Nat Genet. 2011 Jul 20;43(9):847-53. doi: 10.1038/ng.894.
Recombination rates in admixed individuals identified by ancestry-based inference.
Wegmann D1, Kessner DE, Veeramah KR, Mathias RA, Nicolae DL, Yanek LR, Sun YV, Torgerson DG, Rafaels N, Mosley T, Becker LC, Ruczinski I, Beaty TH, Kardia SL, Meyers DA, Barnes KC, Becker DM, Freimer NB, Novembre J.

ZygProb – Zygosity Probability Calculation

ZygProb

:: DESCRIPTION

ZygProb processes convenient and accurate zygosity probability calculation.

::DEVELOPER

Dale R. Nyholt

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Twin Res Hum Genet. 2006 Apr;9(2):194-7.
On the probability of dizygotic twins being concordant for two alleles at multiple polymorphic loci.
Nyholt DR.

RVsharing 1.1.0 – Computes Estimates of the Probability of Related Individuals Sharing a Rare Variant

RVsharing 1.1.0

:: DESCRIPTION

RVsharing computes the probability that a rare variant is shared by related subjects, given that the variant was observed in any of them.

::DEVELOPER

Alexandre Bureau

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • R

:: DOWNLOAD

 RVsharing

:: MORE INFORMATION

Citation

Inferring rare disease risk variants based on exact probabilities of sharing by multiple affected relatives.
Bureau A, Younkin SG, Parker MM, Bailey-Wilson JE, Marazita ML, Murray JC, Mangold E, Albacha-Hejazi H, Beaty TH, Ruczinski I.
Bioinformatics. 2014 Apr 16. pii: btu198.

COAL 2012 – computing Gene Tree Probabilities under the Coalescent process

COAL 2012

:: DESCRIPTION

COAL is a program for computing gene tree probabilities and simulating gene trees in species trees under the coalescent model.

::DEVELOPER

James Degnan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • C Compiler

:: DOWNLOAD

 COAL

:: MORE INFORMATION

Citation

Degnan, JH and LA Salter. 2005.
Gene tree distribtutions under the coalescent process.
Evolution 59(1): 24-37.

MECPM – Maximum Entropy Conditional Probability Moldeling

MECPM

:: DESCRIPTION

MECPM (Maximum Entropy Conditional Probability Moldeling) makes explicit and is determined by the interactions that confer phenotype-predictive power.MECPM achieved both improved sensitivity and specificity for identifying ground-truth markers and interactions.

::DEVELOPER

Computational Bioinformatics & Bio-imaging Laboratory (CBIL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • C Compiler

:: DOWNLOAD

 MECPM

:: MORE INFORMATION

Citation:

Miller, Zhang, Yu, Liu, Chen, Langefeld, Herrington, Wang (2009),
An algorithm for learning maximum entropy probability models of disease risk that efficiently searches and sparingly encodes multilocus genomic interactions
Bioinformatics (2009) 25 (19): 2478-2485.