Sentence examples for using the parsimony method from inspiring English sources
A phylogenetic tree (Fig. 1) was generated from the Clustal W alignment (Figure S1) of the all identified FEZ protein sequences (Table S1) using the parsimony method.
We inferred phylogenetic relationships among isolates by using the parsimony method described previously (Rosenblum et al. 2013).
Phylogenetic trees were reconstructed from these alignments using the NJ algorithm implemented in ClustalX or using the parsimony method (PHYLYP package).
The BLAST program was used to search for nucleotide and amino acid similarities, and phylogenetic analysis was performed using the parsimony method (Phylip package ver. 3.66).
We evaluate the emergence and loss of CPs on a commonly accepted tree of life representation (figure 1), using the parsimony method (see details on the chosen method and other tested ancestral reconstruction methods in the Methods section).
Phylogenetic trees for SS1G_13371 family was generated using the parsimony method with 100 bootstrap replicates with the Extended Majority rule, as implemented in the protpars and consense programs of the Phylip 3.67 package [ 79]. S. sclerotiorum 1980 and B. cinerea b05.10 proteins were clustered based on sequence similarity by Markov clustering using the orthoMCL function in Biolayout 3D [ 80].
Furthermore, to analyze T3E gene histories, we used the parsimony method as implemented in the Mesquite software package [89].
This occurred partly because we used the parsimony method to estimate the minimum numbers of genes in ancestral species.
We used the parsimony method to infer this phylogeny, but the clustering of OTUs is independent of the method of phylogenetic reconstruction used (see Methods).
To infer the tree we used the parsimony method of phylogenetic reconstruction [ 31, 32], but other methods such as neighbor joining (NJ) [ 33] equally support the families.
Since it is quite fast and generates results even if data is noisy and sparse, we decided to use the parsimony method.
