mlRho 2.9 – Estimate the Population Mutation and Recombination Rates from Shotgun-Sequenced Diploid Genomes

mlRho 2.9

:: DESCRIPTION

mlRho takes as input a file with assembled reads from a single diploid individual and returns maximum likelihood estimates of the population mutation rate, $\theta$ , the sequencing error $\epsilon$ , the zygosity correlation, and the population recombination rate, $\rho$

::DEVELOPER

Bernhard Haubold

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX
C Compiler

:: DOWNLOAD

mlRho

:: MORE INFORMATION

Citation

B. Haubold, P. Pfaffelhuber, and M. Lynch.
mlRho: A program for estimating the population mutation and recombination rates from shotgun-sequenced diploid genomes.
Molecular Ecology, 19:277-284, 2010.

HapCUT2 v1.3.1 – Haplotype Assembly or Haplotype Phasing using Sequence Reads from a Diploid Genome

HapCUT2 v1.3.1

:: DESCRIPTION

HapCUT is a max-cut based algorithm for haplotype assembly using sequence reads from the two chromosomes of an individual. It can be applied to sequence data generated from next-generation sequencing platforms. HapCUT takes as input the aligned SAM/BAM files for an individual diploid genome and the list of variants (VCF file), and outputs the phased haplotype blocks that can be assembled from the sequence reads.

::DEVELOPER

Vikas Bansal

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX

:: DOWNLOAD

HapCUT

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Aug 15;24(16):i153-9. doi: 10.1093/bioinformatics/btn298.
HapCUT: an efficient and accurate algorithm for the haplotype assembly problem.
Bansal V, Bafna V.