MMS – Maxent Model Surveyor
Evaluate predictor sets and model complexity for Maxent.
Algal evolution and Coral holobiont biology
Algae data resources
List of available Ostreobium strains and annotated data for the nuclear genome sequence.
Annotations and additional data for the Pedinophyte YPF701 nuclear genome.
A set of UPA and tufA reference sequences for identification of algae in metabarcoding surveys.
Metagenomic data mining
Lean Snakemake workflow for metagenome assembly, annotation and binning.
Indentification of organelle genome contigs from metagenome assemblies.
Flexible and scalable metagenomics pipeline implemented in WDL.
Browse metagenome data and eukaryotic species discovered therein.
Tools for phylogenetics
OrthoFlow, a snakemake workflow for phylogenetic inference of genome-scale datasets of protein-coding genes.
SiteStripper, a Perl script to 'site strip' alignments, i.e. remove a given percentage of fast-evolving sites.
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.
gDAM (graphical Data Availability Matrix), a script that draws a graphical representation of data availability in a concatenated sequence alignment.
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.
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 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 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 coencocytic 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 Phycology47: 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