Category: Genetics & Pedigree

RUNTC – Estimator of First Coalescent Time

RUNTC

:: DESCRIPTION

RUNTC is an estimator of first coalescent time, which is the time when a copy of a gene most recently shared ancestry with other copies of that gene. This is also an estimate of the upper bound of when a mutation has arisen, and it can be used to study the ages of alleles that are found in a population.

::DEVELOPER

the Hey lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

RUNTC

:: MORE INFORMATION

Citation:

Platt A, Pivirotto A, Knoblauch J, Hey J.
An estimator of first coalescent time reveals selection on young variants and large heterogeneity in rare allele ages among human populations.
PLoS Genet. 2019 Aug 19;15(8):e1008340. doi: 10.1371/journal.pgen.1008340. PMID: 31425500; PMCID: PMC6715256.

HKA 20100709 – Statistical Test for Natural Selection

HKA 20100709

:: DESCRIPTION

HKA is a computer program that carries out the widely used statistical test for natural selection.This program can handle very large numbers of loci and sample sizes, and conducts tests via coalescent simulation as well as by the conventional chi square approximation.   The simulations can also be used to conduct other tests of natural selection, including tests of Tajima’s D statistic (1989) and the D statistic of Fu and Li (1993).

::DEVELOPER

the Hey lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

  HKA

:: MORE INFORMATION

IMa3 v1.12 – Generate Posterior Probabilities for complex Demographic Population Genetic Models

IMa3 v1.12

:: DESCRIPTION

IMa2 (Isolation with Migration) implements a method for generating posterior probabilities for complex demographic population genetic models. IMa2 can handle data and implement a model for multiple populations (for numbers of sampled populations between one and ten) – not just two populations (as was the case with the original IM and IMa programs).

IMa3 is the newest in the IM sequence of programs. It can be used to solve a fundamental problem in evolutionary genetics, which is to jointly consider phylogenetic history and pouplation genetic history, including gene exchange.

::DEVELOPER

the Hey lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 IMa3

:: MORE INFORMATION

Citation:

Hey J, Nielsen R. 2007.
Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics.
Proc Natl Acad Sci U S A. 2007 Feb 20;104(8):2785-90.

FPG – Forward Population Genetic Simulation program

FPG

:: DESCRIPTION

FPG (for Forward Population Genetic simulation) simulates a population of constant size that is undergoing various evolutionary processes, including:  mutation, recombination,  natural selection, and migration.   The meaning of “forward” in this context is simply that time, within the simulation, moves forward just as it does in the real world.  This is in contrast to coalescent population genetic simulation in which time, as represented within the simulation, proceeds back into the past.  Coalescent simulations have many advantages, but they are unwieldy if they incorporate natural selection on multiple sites.

::DEVELOPER

the Hey lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

 FPG

:: MORE INFORMATION

WH – Fit Speciation Model to DNA Sequence data sets

WH

:: DESCRIPTION

WH is a computer program that carries out the fitting of a speciation model, and conducts tests of the quality of fit of that model.  The speciation model is called the Isolation Model, and is one without gene flow.  With comparative DNA sequence data from each of two closely related species, the method allows an estimation of the time since speciation and the size of the ancestral species.

::DEVELOPER

the Hey lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX

:: DOWNLOAD

  WH

:: MORE INFORMATION

Sniper 1.6.4 – SNP Discovery Utilizing Multi-mapping Reads

Sniper 1.6.4

:: DESCRIPTION

Sniper is a Bayesian probabilistic model that enables SNP discovery in both unique and repetitive regions of a genome by utilizing the information from multiply-mapped sequence reads.

::DEVELOPER

the Kim Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux/ MacOsX/ Windows
  • Python

:: DOWNLOAD

 Sniper

:: MORE INFORMATION

Citation

Genome Biol. 2011 Jun 20;12(6):R55. doi: 10.1186/gb-2011-12-6-r55.
Sniper: improved SNP discovery by multiply mapping deep sequenced reads.
Simola DF, Kim J.

H2boot beta – Program for Bootstrap Estimates of Quantitative Genetic Data

H2boot beta

:: DESCRIPTION

H2boot is used primarily for parameter estimation and significance testing of individual quantitative genetic parameters using a bootstrapping approach.

::DEVELOPER

Phillips Laboratory at the University of Oregon

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • DOS

:: DOWNLOAD

 H2boot

:: MORE INFORMATION

Citation

Phillips, P.C. and S.J. Arnold. 1999.
Hierarchical comparison of genetic variance-covariance matrices. I. Using the Flury hierarchy.
Evolution 53:1506-1515.

CPCrand beta – Randomization Test of the Common Principal Component Model

CPCrand beta

:: DESCRIPTION

CPCrand is used for comparing variance-covariance matrices derived from different populations using the hierarchical model devised by Bernhard Flury (1988).

::DEVELOPER

Phillips Laboratory at the University of Oregon

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • DOS

:: DOWNLOAD

  CPCrand

:: MORE INFORMATION

Citation

Phillips, P.C. and S.J. Arnold. 1999.
Hierarchical comparison of genetic variance-covariance matrices. I. Using the Flury hierarchy. 
Evolution 53:1506-1515.

rankSynergy – Rank-based Statistical Test for measuring Synergistic Effects between two Gene Sets

rankSynergy

:: DESCRIPTION

The rankSynergy performs a rank-based non-parametric statistical test for measuring the synergistic effects between two gene sets. For calculating an approximate significance value of synergy, an efficient Markov chain Monte Carlo method is used

::DEVELOPER

Yuichi Shiraishi (friend1ws@gmail.com)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

  rankSynergy

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Sep 1;27(17):2399-405. doi: 10.1093/bioinformatics/btr382.
A rank-based statistical test for measuring synergistic effects between two gene sets.
Shiraishi Y, Okada-Hatakeyama M, Miyano S.

PART / PART-up – Test for the Recurrence of Genomic Aberrations

PART / PART-up

:: DESCRIPTION

PART (parametric aberration recurrence test) is a new parametric method to test for the recurrence of genomic aberrations.

PART-up is an  extention of PART to cover unpaired data so that there is a statistical basis for analyzing unpaired genomic data.

::DEVELOPER

Atsushi Niida 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java
  • Perl
  • R package

:: DOWNLOAD

 PART / PART-up

:: MORE INFORMATION

Citation

Niida, A and Imoto, S and Shimamura, T and Miyano, S
Statistical model-based testing to evaluate the recurrence of genomic aberrations
Bioinformatics, 2012, 28:i115-i120