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In comparison with Sudan's work, the GS algorithm provides more linear homogeneous equations in interpolation, thus improving the decoding correction distance.
A neighbor-joining tree was built using MEGA version 5.05 [ 64], adopting the Poisson correction distance.
We used MEGA3 [ 50] to infer the NJ phylogenetic tree, using the pairwise deletion option and Poisson correction distance.
Phylogenetic tree was constructed using MEGA5 (http://www.megasoftware.net) with the neighbor-joining method and the following parameters: pairwise deletion option, 1000 replicates of bootstrap and Poisson correction distance.
Phylogenetic analyses were performed using Neighbour-Joining implemented in MEGA5, using pairwise deletion of gaps and the Poisson correction distance of substitution rates.
The evolutionary divergence between human and mouse orthologous proteins was measured as the number of substitutions per site using the Poisson Correction distance [ 37].
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Poisson correction distances were calculated after all alignment gaps were eliminated.
p-distances (Figure S2) and poisson correction distances (Figure 1A) following the gamma distribution (α = 6.46) were used to construct the phylogenetic trees.
Poisson correction distances (d) were estimated from the equation d = -ln(1 - p), where p represents the proportion of different amino acids.
Published NITR V or I domains were aligned by ClustalW [ 29] and neighbor-joining trees [ 30] were constructed from pairwise Poisson correction distances with 2000 bootstrap replications by MEGA2.1 software [ 31].
The phylogenetic OR gene tree was constructed using MEGA3 software (Kumar et al. 2004) and the Neighbor-Joining (Saitou and Nei 1987) method with the Poisson correction distances and was carried out by 1,000 bootstrap replications.
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