Resources

Algae data resources

Ostreobium genome and strain resources

List of available Ostreobium strains and annotated data for the nuclear genome sequence.
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Pedinophyte YPF701 nuclear genome

Annotations and additional data for the Pedinophyte YPF701 nuclear genome.
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Algal metabarcoding reference data

A set of UPA and tufA reference sequences for identification of algae in metabarcoding surveys.
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Metagenomic data mining

ChloroScan

Snakemake workflow for metagenome binning of chloroplast genomes.
Github

CORGI

Indentification of organelle genome contigs from metagenome assemblies.
Github

Metaphor

Lean Snakemake workflow for metagenome assembly, annotation and binning.
Github

Melbourne Metagenomics Archive

Browse metagenome data and eukaryotic species discovered therein.
Browse

Tools for phylogenetics

OrthoFlow, a snakemake workflow for phylogenetic inference of genome-scale datasets of protein-coding genes.
Github

SiteStripper, a Perl script to 'site strip' alignments, i.e. remove a given percentage of fast-evolving sites.
Github

TreeGradients, a phylogenetic tree drawing program using color or grayscale gradients to trace continuous characters along the tree. It allows for quite sophisticated color ramps.
Github

gDAM (graphical Data Availability Matrix), a script that draws a graphical representation of data availability in a concatenated sequence alignment.
Github

Partitioned Model Tester, a script that facilitates selecting partitioning strategies and models of sequence evolution for phylogenetics. We still provide the software, but be aware that support is discontinued and we recommend IQ-Tree or PartitionFinder for this.
Github

Resources from papers

Original sequence data associated with our research papers gets submitted to ENA/NCBI/DDBJ, and we're not linking to that here. New software that we develop for our work is typically hosted on Github or similar repositories and linked above. The purpose of this list is to post additional resources when we consider they provide substantial added value for the research community, or whenever someone requests them from us. We realise that this list is incomplete, and if there are any resources you think we should add, shoot us an email and we will endeavour to do so.

Get data Bjornson et al. (2026) Stepwise evolutionary transitions in Cladophorales plastid genomes reveal origins of hairpin chromosomes. Current Biology 36: 1659-1674

Get data Hossen et al. (2026) Extensive nuclear datasets resolve the phylogeny of siphonous green algae and identify genome duplications as a contributing factor to evolutionary adaptations. New Phytologist 250: 1918-1933

Get data Hastings et al. (2026) Enhancing species discovery and description in algal turfs: a case study in the green alga Pseudoderbesia (Bryopsidales). Journal of Phycology 62: 222-232

Get data Verbruggen et al. (2025) Scaling up species delimitation from DNA barcodes to whole organelle genomes: strong evidence for discordance among genes and methods for the red alga Dasyclonium. Molecular Ecology Resources 25: e14132

Get data Verbruggen et al. (2025) Extensive diversity of Symbiochlorum-related algae from environmental sequences and culture strains supports the description of the new family Symbiochloraceae (Ulvophyceae, Chlorophyta). Journal of Phycology 61: 926-932

Get data Uthanumallian et al. (2024) Genome-wide patterns of selection-drift variation strongly associate with organismal traits across the green algae. Genome Research 34: 1130-1139

Get data Hsieh et al. (2024) Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches. npj Systems Biology and Applications 10: 54

Get data Vieira et al. (2021) Global biogeography and diversification of a group of brown seaweeds (Phaeophyceae) driven by clade-specific evolutionary processes. Journal of Biogeography 48: 703-715

Get data Rindi et al. (2020) Phylogeography of the Mediterranean green seaweed Halimeda tuna. Journal of Phycology 56: 1109-1113

Get data Bringloe et al. (2020) Phylogeny and evolution of the brown algae. Critical Reviews in Plant Sciences 39: 281-321

Get data Leliaert et al. (2018) Patterns and drivers of species diversity in the Indo-Pacific red seaweed Portieria. Journal of Biogeography 45: 2299-2313

Get data del Cortona et al. (2017) The plastid genome in Cladophorales green algae is encoded by hairpin plasmids. Current Biology 27: 3771-3782

Get data Verbruggen & Costa (2015) Molecular survey of Codium species diversity in southern Madagascar. Cryptogamie Algologie 36: 171-187

Get data Verbruggen & Costa (2015) The plastid genome of the red alga Laurencia. Journal of Phycology 51: 586-589

Get data Verbruggen et al. (2013) Improving transferability of introduced species’ distribution models: new tools to forecast the spread of a highly invasive seaweed. PLoS One 8: e68337

Get data Ciancia et al. (2012) Characterization of cell wall polysaccharides of the coenocytic green seaweed Bryopsis plumosa (Bryopsidaceae, Chlorophyta) from the Argentine coast. Journal of Phycology 48: 326-335

Get data Oliveira-Carvalho et al. (2012) Phylogenetic analysis of Codium species from Brazil, with the description of the new species C. pernambucensis (Bryopsidales, Chlorophyta). European Journal of Phycology 47: 355-365

Get data Verbruggen et al. (2012) The new species Codium recurvatum from Tanzania. European Journal of Phycology 47: 216-222

Get data Verbruggen & Schils (2012) Rhipilia coppejansii, a new coral reef-associated species from Guam (Bryopsidales, Chlorophyta). Journal of Phycology 48: 1090-1098

Get data Coppejans et al. (2011) Rhipidosiphon lewmanomontiae sp. nov. (Bryopsidales, Chlorophyta), a calcified udoteacean alga from the central Indo-Pacific based on morphological and molecular investigations. Phycologia 50: 403-412

Get data Verbruggen et al. (2010) Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life. BMC Evolutionary Biology 10: 16

Get data Verbruggen et al. (2009) Macroecology meets macroevolution: evolutionary niche dynamics in the seaweed Halimeda. Global Ecology and Biogeography 18: 393-405

Get data Cocquyt et al. (2009) Gain and loss of elongation factor genes in green algae. BMC Evolutionary Biology 9: 39

Get data Verbruggen et al. (2009) Phylogenetic analysis of Pseudochlorodesmis strains reveals cryptic diversity above the family level in the siphonous green algae (Bryopsidales, Chlorophyta). Journal of Phycology 45: 726-731

Get data Verbruggen et al. (2009) A multi-locus time-calibrated phylogeny of the siphonous green algae. Molecular Phylogenetics and Evolution 50: 642-653

Get data Verbruggen et al. (2007) Halimeda pygmaea and Halimeda pumila (Bryopsidales, Chlorophyta): two new dwarf species from fore reef slopes in Fiji and the Bahamas. Phycologia 46: 513-520