PhyloSort

[…] aligned via mafft v641, and used for phylogenetic reconstruction under the protgammalg evolutionary model of raxml v.7.2.830. the resulting trees were sorted for patterns of monophyly using phylosort. a multi-protein alignment of length 25,143 amino acids was produced by sampling our in-house database for homologs to the 458 cegs. each individual ceg family was aligned with its mast-4 […]

[…] file s2, supplementary material online). raxml 7.2.8 () was run to reconstruct the phylogenetic trees, with lg substitution matrix + γ4 + f evolutionary model with 100 bootstrap replicates. phylosort () was used to cluster the repetitive phylogenetic trees for the queries with multiple paralogs. the 49 reconstructed phylogenies divided into four clusters corresponding to the four […]

[…] species were also removed because monophyly could not be assessed and to mitigate any potential signal from contamination. for each tree, dinoflagellate nearest neighbors were identified using phylosort, a tool for sorting phylogenetic trees by searching for a user-specified grouping of interest (). for this analysis, a nearest neighbor association is defined as a sister relationship […]

[…] algal genes (). this was based on basic local alignment search tool (blast) analysis against the nonredundant national center for biotechnology information (ncbi) database and also by using phylosort, a phylogenomic pipeline designed to identify candidates of gene transfer (). although a handful of putatively transferred genes (mostly of bacterial or viral origin) emerged […]

[…] synergistetes, thermotogae and verrucomicrobia). then phylogenies were inferred as described in the phylogenetic analyses (above) except alignments were refined using gblocks . finally, using phylosort , ml trees were grouped into different phylogenetic categories by matching topological criteria with at least 50% bootstrap support values, the topological criteria were defined to examine […]