Author: Stagegaard, Julia; Kurth, Andreas; Stern, Daniel; Dabrowski, Piotr Wojciech; Pocknell, Ann; Nitsche, Andreas; Schrick, Livia
Title: Seasonal recurrence of cowpox virus outbreaks in captive cheetahs (Acinonyx jubatus) Document date: 2017_11_9
ID: 0oa4x05s_10
Snippet: For phylogenetic analysis, an alignment of the assembled genomes with all CPXV full genomes and a single representative sequence of every other OPV species available in Gen-Bank was performed by using mafft [21] . In order to remove spurious phylogenetic signals, low-quality alignment regions were stripped from the alignment by using GBlocks [22] , yielding a stripped alignment of 136,924 gap-free positions. A phylogenetic tree was then calculate.....
Document: For phylogenetic analysis, an alignment of the assembled genomes with all CPXV full genomes and a single representative sequence of every other OPV species available in Gen-Bank was performed by using mafft [21] . In order to remove spurious phylogenetic signals, low-quality alignment regions were stripped from the alignment by using GBlocks [22] , yielding a stripped alignment of 136,924 gap-free positions. A phylogenetic tree was then calculated from this stripped alignment by using PhyML [23] (GTR+É£, 4 substitution rate categories, aLRT branch supports).
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