Fig. 1b. Dated phylogeny of Convolvuleae inferred in beast from analysis of the concatenated ITS, matK and rbcL dataset. Node bars represent 95 % HPD estimates. Scale bar represent millions of years before present. Coloured branches and taxon names indicate the distribution area inferred in Lagrange, as shown in Fig. 1a. Black branches indicate ambiguous areas (less than 0.2 lnL difference between first and second most likely distribution). Grey branches indicate a multiple area distribution. Numbers at the top-left of nodes are referred to in Table 1. * indicate the location of calibrated nodes. Black circles on nodes indicate nodes with Bayesian Posterior Probabilities of at least 0.95
Fig. 2. Nucleotide evolution for the N gene of aMPV, indicated by the nucleotide substitution rates found for the U.S. aMPV group C and U.S. aMPV group A. Grey bar indicates the group C phylogeny in Fig. 1a, and black bar indicates the group A phylogeny in Fig. 1d. a) Site frequency spectra (SFS) for U.S. aMPV group C (including members collected in the U.S. during the 2014–2017 and 2017–2018 seasons). The mean of the SFS (black) was plotted on top of the SFS of the group-specific branch leading to the root of the group. b) SFS of the N gene of U.S. aMPV group C (including members collected during the 2014–2017 and 2017–2018 seasons).
Use this link to download the Lagrange optimisation programme: https://github.com/synthetos/Lagrange Use this link to download the Beast optimisation programme: https://github.com/synthetos/Beast_2 Use this link to download the Beast2 source code: http://github.com/synthetos/beast2
In the last section of Table 1, we show the results for our most recent analysis. For the previous analysis, see Coates et al. (2012). For more details about the BEAST methodology, see the website.
A recent issue of TreeBASE (2019-3) includes the BEAST 2 team paper describing the BEAST 2 software and a JSON file with relevant metadata for v2.7.X. The BEAST 2 team paper describes the integration of BEAST 2 into the existing BEAST 2 software and some of its new features.
S. McKain described a method for creating a phylogenetic tree of the 20 haplotypes of an HLA locus. The paper is available here: Phylogenetic analysis of 20 HLA-B haplotypes using Bayesian phylogenetic methods with BEAST
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