Tool stats & trends
Looking to identify usage trends or leading experts?
|Interface||Command line interface|
|Restrictions to use||None|
|Input data||A table of counts of the four nucleotides at every position.|
|Output data||Some shotgun reads.|
No version available
- person_outline Bernhard Haubold
Publication for mlRho
Genetic Ancestry of Hadza and Sandawe Peoples Reveals Ancient Population Structure in Africa
[…] site, F^ST= is half of the pairwise distance from TreeMix, and N˜e is the harmonic mean of the estimated effective population sizes N^e (), assuming that F^ST=0 at t=0 (). We estimated N^e using the mlrho autosomal heterozygosities H^ reported in the Simons Genome Diversity Project () and the relationship θ^=H^1−H^. The Simons Genome Diversity Project did not include individuals representing Cush […]
Genotype Calling from Population Genomic Sequencing Data
[…] les of the 83 clones from the processed BAM files using Samtools. The pro files of nucleotide read quartets were made from the mpileup files using sam2pro (version 0.8) (http://guanine.evolbio.mpg.de/mlRho/sam2pro_0.8.tgz). The input file of nucleotide read quartets of 83 clones was made from the pro files using GFE (). To avoid analyzing misassembled regions, we excluded regions considered to be […]
Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L.
[…] ow depth of coverage may lead to missing minor alleles, which would result in an underestimation of diversity. Finally, the small decrease in theta with increasing depth, when theta is estimated with mlrho and when paralogous loci are removed, can be explained by a sampling effect, because, at high depth, fewer alleles are considered in the analysis, accounting for lower estimates of diversity.Our […]
Deciphering the Wisent Demographic and Adaptive Histories from Individual Whole Genome Sequences
[…] Genetic heterozygosities were estimated from the individual genome alignments onto the UMD 3.1 cattle assembly (i.e., based on the mpileup files described above) using mlrho version 2.8 (). Note that mlrho actually implements a maximum likelihood estimator of the population mutation rate (θ=4Neμg), which fairly approximates heterozygosity under an infinite sites mod […]
Human adaptation and population differentiation in the light of ancient genomes
[…] 00 generations in the history of each population. We infer these Ne based on the observed heterozygosity in the two ancient European samples. We first fitted the heterozygosity measured in Loschbour (mlrho) in Lazaridis et al. to neutral simulations using our demographic model. For each Ne, ranging from 50 to 5,000 in steps of 50, we ran 100,000 simulations and calculated the expected heterozygosi […]
Whole genome re sequencing of date palms yields insights into diversification of a fruit tree crop
[…] ples with little or no evidence of admixture in the STRUCTURE analysis. Single genome-based estimates of the population mutation rate θ were obtained directly from each of the sample alignments using mlRho (version 2.7); (). Per-individual inbreeding coefficients were estimated using ngsF with genotype likelihoods generated by ANGSD provided as input. Differences in θW and Tajima's D between genom […]
Looking to check out a full list of citations?
Be the first to review mlRho