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It involves two steps the removal of noise from the sequencing itself and the removal of PCR point errors.
This project also includes the Perseus algorithm for chimera removal.
ANGSD is a software for analyzing next generation sequencing data.
The software can handle a number of different input types from mapped reads to imputed genotype probabilities.
Apollo allows researchers to explore genomic annotations at many levels of detail, and to perform expert annotation curation, all in a graphical environment.
This graph representation retains ambiguities, such as those arising from polymorphism, uncorrected read errors, and unresolved repeats, thereby providing information that has been absent from previous genome assemblies.https://umn.edu/sw/Allpath Amplicon Noise is a collection of programs for the removal of noise from 454 sequenced PCR amplicons.This program was developed to remove residual adapter sequences from next generation sequencing reads.The program handles both single end and paired end data. 2012) is a software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates. is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets.
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It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm.