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For SP, the maximum connection limit was ignored, forcing all sequences to be connected in a single network.
Statistical parsimony analysis of the full ITS alignment resulted in a single, highly interconnected and largely unresolved network with maximum connection limit of 9 steps (Figure 3).
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The estimated statistical parsimony network, which had a maximum calculated connection limit of 14 steps (at 95% confidence), is shown in Figure 2. It was congruent in its general topology with a phylogeny estimated by Bayesian inference (BI), which had low branch support (similar to [ 15]) (not shown).
Statistical parsimony estimates the maximum number of single substitutions among haplotypes (referred to as the connection limit) preceded by the connection of haplotypes into a network differing by increasing numbers of single site changes [ 94].
A maximum parsimony network was constructed using TCS 1.21 [ 70] with a 95% connection limit.
An estimated phylogeny using the maximum likelihood optimality criterion showed the same topology, and a statistical parsimony network, constructed using TCS with the 95% connection limit, yielded several disconnected networks (not shown).
A maximum likelihood phylogenetic tree of the haplotypes for each gene was constructed using MEGA 5.2 [ 35], and a haplotype network was built using the TCS program [ 36] (95% connection limit; gaps treated as a fifth state) to assess the potential connection between haplotypes and resistance phenotypes.
We used the default settings of a 95% connection limit.
The higher connection limit mirrored the GMYC results.
A 95% connection limit probability was used, where gaps were treated as missing with no connection limit step priors.
TCS results varied depending on the connection limit: a 95% connection limit resulted in fewer independent networks compared to a 99% limit.
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