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mlRho specifications

Information


Unique identifier OMICS_24622
Name mlRho
Software type Application/Script
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.
Output format FASTA
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Version 2.9
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Bernhard Haubold

Publication for mlRho

mlRho citations

 (10)
call_split

Genetic Ancestry of Hadza and Sandawe Peoples Reveals Ancient Population Structure in Africa

2018
Genome Biol Evol
PMCID: 5863221
PMID: 29608727
DOI: 10.1093/gbe/evy051
call_split See protocol

[…] 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 […]

library_books

Genotype Calling from Population Genomic Sequencing Data

2017
PMCID: 5427492
PMID: 28108551
DOI: 10.1534/g3.117.039008

[…] 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 […]

library_books

Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L.

2016
Ecol Evol
PMCID: 5513258
PMID: 28725400
DOI: 10.1002/ece3.2466

[…] 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 […]

call_split

Deciphering the Wisent Demographic and Adaptive Histories from Individual Whole Genome Sequences

2016
Mol Biol Evol
PMCID: 5062319
PMID: 27436010
DOI: 10.1093/molbev/msw144
call_split See protocol

[…] 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 […]

call_split

Human adaptation and population differentiation in the light of ancient genomes

2016
Nat Commun
PMCID: 4802047
PMID: 26988143
DOI: 10.1038/ncomms10775
call_split See protocol

[…] 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 […]

library_books

Whole genome re sequencing of date palms yields insights into diversification of a fruit tree crop

2015
Nat Commun
PMCID: 4667612
PMID: 26549859
DOI: 10.1038/ncomms9824

[…] 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 […]

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mlRho institution(s)
Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany; Mathematical Institute, Albert-Ludwigs University, Freiburg, Germany; Department of Biology, Indiana University, Bloomington, IN, USA
mlRho funding source(s)
Supported by the German Federal Ministry of Education and Research (BMBF) through the Freiburg Initiative for Systems Biology (0313921), the National Institutes of Health (NIH) (R01 GM036827) and the National Science Foundation (NSF) (EF-0827411).

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