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Characterization of Genetic Variability of Venezuelan Equine Encephalitis Viruses
[…] We used the genotype data from genomic sequences to create maximum parsimony phylogenetic trees, using Parsimonator (https://github.com/stamatak/Parsimonator-1.0.2). We generated 100 trees using different random number seeds, and selected the most parsimonious (that is, the tree requiring the smallest […]
ncRNA orthologies in the vertebrate lineage
[…] aforementioned strategy in a reasonable amount of time. For these families we build fast trees using FastTree2 () with options -nt -quiet -nopr and RaxML-Light (version 1.0.6) () in combination with Parsimonator v.1.0.2 (http://sco.h-its.org/exelixis/software.html), a lightweight and fast implementation for building starting trees for RAxML under parsimony (with options -p 12345). When built base […]
Evolution and selection of Rhg1, a copy number variant nematode resistance locus
[…] od with 10 000 bootstrap replicates to assess reliability of clustering, using mega 6.0 (Tamura et al. ). Clustering of germplasm accessions from the much larger Infinium data set was performed using parsimonator version 1.0.2 (https://github.com/stamatak/Parsimonator-1.0.2). Ten SNPs for each taxon located between 1 620 585 and 1 712 832 bp on chromosome 18 were used for the phylogenetic analysis […]
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