TREE2FASTA: a flexible Perl script for batch extraction of FASTA sequences from exploratory phylogenetic trees - PubMed (original) (raw)

TREE2FASTA: a flexible Perl script for batch extraction of FASTA sequences from exploratory phylogenetic trees

Thomas Sauvage et al. BMC Res Notes. 2018.

Abstract

Objective: The body of DNA sequence data lacking taxonomically informative sequence headers is rapidly growing in user and public databases (e.g. sequences lacking identification and contaminants). In the context of systematics studies, sorting such sequence data for taxonomic curation and/or molecular diversity characterization (e.g. crypticism) often requires the building of exploratory phylogenetic trees with reference taxa. The subsequent step of segregating DNA sequences of interest based on observed topological relationships can represent a challenging task, especially for large datasets.

Results: We have written TREE2FASTA, a Perl script that enables and expedites the sorting of FASTA-formatted sequence data from exploratory phylogenetic trees. TREE2FASTA takes advantage of the interactive, rapid point-and-click color selection and/or annotations of tree leaves in the popular Java tree-viewer FigTree to segregate groups of FASTA sequences of interest to separate files. TREE2FASTA allows for both simple and nested segregation designs to facilitate the simultaneous preparation of multiple data sets that may overlap in sequence content.

Keywords: Barcoding; Biodiversity; Clone; Contaminant; Cryptic; Environmental; FigTree; Forensic; Metabarcoding; OTU; Phylogeny; Systematics.

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Figures

Fig. 1

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

Fig. 2

Fig. 2

Sorting Genbank 16S rDNA for red seaweeds with TREE2FASTA. a Successive edits done in FigTree to establish an annotated design nested by color for reference and environmental red seaweeds (Florideophytes). b Folders and subsetted FASTA files output by TREE2FASTA for downstream analyses (folder content separated by dashed lines). For figure clarity, the Florideophyceae annotation was abbreviated to ‘Flo’ within FASTA file icons. The tree was produced with the 500 closest matches to Taenioma perpusillum (MF101452) on Genbank®

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