polyHap 2 – Phase Polyploids and Copy Number Regions

polyHap 2

:: DESCRIPTION

polyHap is a program for phasing polyploids and copy number regions. PolyHap allows each individual to have a different ploidy, but ploidy cannot vary over the genomic region analysed. It employs a hidden Markov model (HMM) and a sampling algorithm to infer haplotypes jointly in multiple individuals and to obtain a measure of uncertainty in its inferences.

::DEVELOPER

Dr Lachlan J Coin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
Java

:: DOWNLOAD

polyHap

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Jun 1;26(11):1437-45. doi: 10.1093/bioinformatics/btq157. Epub 2010 Apr 20.
Inferring combined CNV/SNP haplotypes from genotype data.
Su SY1, Asher JE, Jarvelin MR, Froguel P, Blakemore AI, Balding DJ, Coin LJ.

Shu-Yi Su et al.
Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions
BMC Bioinformatics 2008, 9:513

PHASE 2.0 – Bayesian & Maximum Likelihood Phylogenetic Inference Package

PHASE 2.0

:: DESCRIPTION

PHASE (PHylogenetics And Sequence Evolution) is a package that performs molecular phylogenetic inference. The software seeks to accurately compare molecular sequences to determine the likely evolutionary relationships between a group of species.This package is designed specifically for use with RNA sequences that have a conserved secondary structure, e.g., rRNA and tRNA. It is well known that compensatory substitutions occur in the paired regions of RNA secondary structures; this means that substitutions occurring on one side of a pair are correlated with substitutions on the other side. Most phylogenetic programs assume that each site in a molecule evolves independently of the others but this assumption is not valid for RNA genes.

::DEVELOPER

Rattray Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOS

:: DOWNLOAD

PHASE

:: MORE INFORMATION

Citation

V. Gowri-Shankar and M. Rattray.
A reversible jump method for Bayesian phylogenetic inference with a non-homogeneous substitution model” Molecular Biology and Evolution
Molecular Biology and Evolution 24(6):1286-1299 (2007).

ENT 1.0.2 – Genotype Phasing by Entropy Minimization

ENT 1.0.2

:: DESCRIPTION

ENT is a highly scalable genotype phasing algorithm based on entropy minimization. ENT is capable of phasing both unrelated and related genotypes coming from complex pedigrees.

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

Linux

:: DOWNLOAD

ENT

:: MORE INFORMATION

Citation:

A. Gusev and I.I. Mandoiu and B. Pasaniuc,
Highly Scalable Genotype Phasing by Entropy Minimization,
IEEE/ACM Trans. on Computational Biology and Bioinformatics 5, pp. 252-261, 2008

PHASE 2.1.1 – Haplotype Reconstruction & Recombination Rate Estimation

PHASE 2.1.1

:: DESCRIPTION

PHASE is a software for haplotype reconstruction, and recombination rate estimation from population data.

::DEVELOPER

Matthew Stephens Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Mac

:: DOWNLOAD

PHASE ; Manual

:: MORE INFORMATION

The software is free for non-commercial use, and may be licensed for commercial use.