Fig. 1

Simulated phylogeny displaying taxa named ‘A’ to ‘T’. a Basic workflow for FASTA sequence extraction with TREE2FASTA. An exploratory tree is built following multiple-alignment of FASTA data. The Newick tree string (NWK) is visualized and edited in the tree-viewer FigTree and saved as a NEXUS file (NEX). TREE2FASTA uses the FASTA alignment and the NEXUS file (NEX) to produce subsetted FASTA files according to user selection scheme (here color). b Example of possible color and/or annotation selection schemes in FigTree for TREE2FASTA sequence extraction. The FASTA icon marked with an asterisk ‘*’ contains FASTA sequences for taxa H and I lacking color selection (i.e. achromatic) or lacking annotation. For figure clarity annotation ‘Group1’ to ‘Group4’ are reported G1 to G4 within FASTA file icons. FASTA files output to different folders are delimited by dashed boxes