Glossary

Terms used in the T-BAS interface and documentation.

Backbone constraint tree with bootstraps — RAxML method Bifurcating tree — Tree where each node has 2 children BLAST — Basic Local Alignment Search Tool, used to match unknown sequences to known sequences in database De novo phylogenetic analysis — RAxML method EPA with likelihood weights — RAxML method that places sequence on edges of existing tree FASTA — A file sequence format for unaligned data Genetic distance cutoff — Value used by custom algorithm to exclude divergent species from placement GTRCAT — Rate-heterogeneity model; faster approximation than GTRGAMMA GTRGAMMA — General Time Reversible model with Gamma-distributed rates across sites ITS — Internal transcribed spacer locus Labels: Display Names — Node-click context menu; show leaf names for selected clade; large trees (>2000 leaves) may hide names for performance Labels: Likelihood Weight — Node-click context menu; for an EPA placement leaf, show leaves on the edge that sum to 95% cumulative weight Ladderize tree — Sort tree leaves from deepest to shallowest (or reverse) Locus (Loci) — A location on a chromosome LSU — Large subunit locus MEP — Metadata Enhanced PhyloXML; valid PhyloXML with added tags for T-BAS/DeCIFR Metadata: Download — Node-click context menu; download selected data in chosen format/sequence options Metadata: View — Node-click context menu; view selected data in pop-up window Multifurcating tree — Tree where nodes can have multiple children NEWICK — A standard for representing trees NEXUS — A file format that can contain trees and alignments OTUs — Operational groupings of sequences (often by % similarity) Outgroup — Leaves in a distinct clade used to root a tree PHYLIP — A file format for aligned sequence data PhyloXML — XML language for phylogenetic trees (or networks) and associated data Query sequences — Unaligned unknown sequence data Rate heterogeneity model — A phylogenetic model that accounts for rate heterogeneity across sites RAxML — Software used for placement and other phylogenetic utilities Reference set — Tree + alignments + metadata for known taxa at a scope/level Taxa: Select All — Node-click context menu; select all leaves on tree Taxa: Select (unselect) — Node-click context menu; select or unselect all leaves in a clade Taxa: Unselect All — Node-click context menu; unselect all leaves on tree Tree: Collapse (expand) — Node-click context menu; collapse/expand a clade Tree: Network (TCS) — Node-click context menu; create a TCS network of query strains in a clade Tree: Newick tree — Node-click context menu; download a Newick subtree (PHYLIP or NEXUS options may be available) Tree: Phylogeny (RAxML) — Node-click context menu; create a de novo tree for selected clade Tree: Pie Charts — Node-click context menu; create pie charts summarizing selected attributes Tree: Subtree (new window) — Node-click context menu; view subtree in a new window Tree: Subtree (tree) — Node-click context menu; view subtree UNITE — Database of fungal ITS for BLAST