PhyloSort

[…] in is also considered as the support for the opposing bacterial clade (Proteobacteria + Cyanobacteria) on the tree. This is distinct from the assumption of the lowest common ancestor for a clade in PhyloSort (), in which subtree-rooting could be invoked during a search.Existing utilities identify clades of interest without considering the occurrence of the target leaves elsewhere on the tree. Fo […]

[…] HGT between co-occurring extremophilic bacteria and archaea () or HGT of cyanobacterial origin into the genomes of green algae (). Several programs have implemented similar search processes including PhyloSort (), Pyphy (), PhyloGenie () and most recently PhySortR (). However, in order to identify and summarize multiple evolutionary signals in a set of gene trees (e.g., all putative cases of HGT, […]

[…] selected, 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 pe […]

[…] lementary 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 protein […]

[…] ellate 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 betwee […]

[…] ansferred 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 from these anal […]