LAMARC 2.1.10 – Maximum Likelihood & Bayesian Estimation of Population Parameters

LAMARC 2.1.10

:: DESCRIPTION

LAMARC (Likelihood Analysis with Metropolis Algorithm using Random Coalescence) is a program which estimates population-genetic parameters such as population size, population growth rate, recombination rate, and migration rates. It approximates a summation over all possible genealogies that could explain the observed sample, which may be sequence, SNP, microsatellite, or electrophoretic data.

::DEVELOPER

Felsenstein/Kuhner lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX

:: DOWNLOAD

LAMARC

:: MORE INFORMATION

Citation:

Mary K. Kuhner
LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters
Bioinformatics (2006) 22 (6): 768-770.

PKreport 1.5 – Reporting Pipeline for Checking Population Pharmacokinetic Model Assumption

PKreport 1.5

:: DESCRIPTION

PKreport aims to 1) provide automatic pipeline for users to visualize data and models. It creates a flexible R framework with automatically generated R scripts to save time and cost for later usage; 2) implement an archive-oriented management tool for users to store, retrieve and modify figures. 3) offer powerful and convenient service to generate high-quality graphs based on two R packages: lattice and ggplot2.

::DEVELOPER

Xiaoyong Sun <johnsunx1 at gmail.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows /MacOsX
  • R

:: DOWNLOAD

 PKreport

:: MORE INFORMATION

Citation:

BMC Med Inform Decis Mak. 2011 May 16;11:31. doi: 10.1186/1472-6947-11-31.
PKreport: report generation for checking population pharmacokinetic model assumptions.
Sun X1, Li J.

jPopGen 1.0b7 – Collection of Java programs for Population Genetic Analysis

jPopGen 1.0b7

:: DESCRIPTION

jPopGen Suite is an integrated tool for population genetic analysis of DNA polymorphisms from nucleotide sequences.

::DEVELOPER

Xiaoming Liu, Ph.D.(xmliu.uth{at}gmail.com)

:: SCREENSHOTS

jPopGen

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 jPopGen

:: MORE INFORMATION

Citation:

Methods Ecol Evol. 2012 Aug 1;3(4):624-627. Epub 2012 Mar 2.
jPopGen Suite: population genetic analysis of DNA polymorphism from nucleotide sequences with errors.
Liu X.

Partition 2.0 / PartitionML / PartitionView – maximum likelihood / Identifying Population Sub-division & Assigning Individuals to Populations

Partition 2.0 / PartitionML / PartitionView

:: DESCRIPTION

Partition is a model-based statistical software package for identifying population sub-division and assigning individuals to populations, on the basis of their genotypes at co-dominant marker loci. The underlying population genetic model is appropriate for out-crossing diploid organisms.

PartitionML is a program that searches for the best possible partition of a sample into independent panmictic clusters and simultaneously assign individuals to them using a maximum likelihood (ML) criterion.

PartitionView will read the  partition output file, as it is being written, and will display the path of the Markov chain (see below) as it evolves in real time.

::DEVELOPER

Partition team

:: SCREENSHOTS

Partition

PartitionView

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 Partition  / PartitionML

:: MORE INFORMATION

Citation

Heredity (Edinb). 2009 Jul;103(1):32-45. doi: 10.1038/hdy.2009.29. Epub 2009 Apr 1.
An agglomerative hierarchical approach to visualization in Bayesian clustering problems.
Dawson KJ1, Belkhir K.

Heredity (Edinb). 2002 Jul;89(1):27-35.
Heterozygote deficiencies in small lacustrine populations of brook charr Salvelinus Fontinalis Mitchill (Pisces, Salmonidae): a test of alternative hypotheses.
Castric V1, Bernatchez L, Belkhir K, Bonhomme F.

MML – Haplotyping using both Family and Population Infomation

MML

:: DESCRIPTION

MML (Mendalian Constrained Maximum Likelihood) is a software to analyze haplotype polymorphisms in a real human population.

::DEVELOPER

Xin Li 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 MML

:: MORE INFORMATION

Citation

Xin Li, Yixuan Chen and Jing Li.
Detecting Genome-wide Haplotype Polymorphism by Combined Use of Mendelian Constraints and Local Population Structure.
Pacific Symposium on Biocomputing 15:348-358(2010).

iAdmix 1.0 – Using population allele frequencies for Computing Individual Admixture Estimates

iAdmix 1.0

:: DESCRIPTION

iAdmix is a program to estimate individual admixture proportions from DNA sequencing experiments (exome sequencing, targeted sequencing, low coverage whole-genome sequencing or genotyping)

::DEVELOPER

Bansal Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

 iAdmix

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2015 Jan 16;16(1):4.
Fast individual ancestry inference from DNA sequence data leveraging allele frequencies for multiple populations.
Bansal V, Libiger O.

Adapt-A-Rate 1.0 – Estimate the Rate of Adaptive Fixation in Population

Adapt-A-Rate 1.0

:: DESCRIPTION

Adapt-A-Rate is a program to estimate the rate of adaptive fixation in a population from sequences sampled at different points in time.

::DEVELOPER

Samir Bhatt and Oliver Pybus

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 Adapt-A-Rate

:: MORE INFORMATION

Citation:

Bhatt S, Holmes EC, Pybus OG (2011)
The genomic rate of molecular adaptation of the human influenza A virus.
Molecular Biology & Evolution In press

iRep v1.10 – Estimating Bacteria Replication Rates based on Population Genome Copy Number Variation

iRep v1.10

:: DESCRIPTION

iRep is a method for determining replication rates for bacteria from single time point metagenomics sequencing and draft-quality genomes.

::DEVELOPER

Banfield Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux/windows /MacOsX
  • Python

:: DOWNLOAD

iRep

:: MORE INFORMATION

Citation

Brown CT, Olm MR, Thomas BC, Banfield JF.
Measurement of bacterial replication rates in microbial communities.
Nat Biotechnol. 2016 Dec;34(12):1256-1263. doi: 10.1038/nbt.3704. Epub 2016 Nov 7. PMID: 27819664; PMCID: PMC5538567.