phylogeny-flow 0.1.0-r1 inferred a phylogenetic tree from a set of homologous protein sequences.

Input sequences were first normalized to safe sequence identifiers, aligned with mafft, and then processed by the selected trimming step.
The alignment trimming mode was trimal (automated1). Tree inference used iqtree. The canonical final Newick tree is 03_results/tree/tree.nwk.

Static tree plots were generated with taf-bioconductor-bioviz bioviz-tree using journal style, rectangular primary layout, rectangular,circular gallery layouts, none label alignment, pretty label transform, and formats pdf,png,svg.

This flow assumes the input sequences are homologous. The inferred tree is a gene/protein tree under the selected alignment, trimming and tree-inference settings; it should not be interpreted automatically as a species tree.