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We calculated branch orders for the ddaA, ddaB and ddaF neurons (Table 2).
Following Perez-Barbería et al. [54], we calculated branch lengths using three different methods [55], [56], [57].
We calculated branch ages using the divergence times estimated by BEAST.
For comparison, we also calculated branch lengths for an RNAP2 dataset from 12 Drosophila species with the topology from [ 14].
We first calculated branch lengths of the ML topology using the Cyt b data with a substitution model and parameters inferred using Modeltest.
To analyse this issue, we calculated branch lengths for 1199 orthologous groups comprising sequences from Tribolium and Drosophila, using human as an outgroup.
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Thus, we have shown that experimental SP dispersion, shown in dots in Fig. 5, obtained from the ATR spectra is in reasonable agreement with calculated branches.
From the calculated branching ratios, it was found that TCE and cis-dichloroethene (cis-DCE) were dominantly dechlorinated to chloroacetylene and acetylene, respectively, through reductive elimination for both columns.
We calculated branch-specific protein divergence and expression divergence as described above for each branch in the amniote species tree, while leaving out chimpanzee, gorilla, and orangutan to avoid short branch lengths.
The OU and Pagel's λ fitting procedures calculate branch length transformation parameters, d for the OU process that is a function of time and λ for Pagel's transformation, which is constant across the tree, by restricted maximum likelihood (REML).
Rapid bootstrap implemented in RAxML was used to calculate branch support for the species tree.
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