This process was performed using a web interface tool described in the alignments procedures section of the methods, where the data on the alignments are reported and graphically displayed.
Re-estimate the leaf values and HMM transition parameters based on the alignments from four and most recent DTAMs. 6.
SB holds patents on the alignments of fragmentation trees, whose value might be affected by the present manuscript.
Full details on the alignments compiled for the present study are given in supplemental Table S1.
Based on the alignments, a distance matrix was constructed using DNAdist from the PHYLIP 3.6 package [15] with the default parameters in the Jukes-Cantor model option [16].
Gene structures were defined based on the alignments obtained, the conserved positions of introns in homologous bZIP genes, and the presence of canonical splicing sites (GT-AG).
Based on the alignments of the concatenated MLST gene fragments comprising 3284 sites with 383 parsimony informative sites SplitsTree4 [55] was used to construct a neighbor-net [56].
We also computed maximum-likelihood trees on the alignments to assess the difference in reconstruction accuracy between simple distance-based and character-based approaches.
Subsequently, we used the neighbor-joining method with 1000 bootstraps on the alignments with the programs SEQBOOT, DNADIST, PROTDIST, NEIGHBOR, and CONSENSE in the PHYLIP 3.65 software package.
For example, to assess the accuracy of the trees based on the alignments, we compared the taxonomic assignments for each sequence with the structure of the phylogenetic tree.
Based on the alignments, phylogenetic trees were constructed using the neighbor-joining method with 1000 bootstrap replicates using the MEGA 3.1 program.
