• Tool to explore the copy-number gene family variation between two groups of species.
• Easily detect gene family expansions between two groups of organisms (each group contains one or more organisms). Thus it is easy to explore gene families with a large copy number in one phylogenetic clade compared to another phylogenetic clade. For each small square in the expansion plot, there is a corresponding copy number in organism group 1 (X-axis) and a corresponding copy number in organism group 2 (Y-Axis), respectively. The color of the square indicates how many gene families in PLAZA have those copy numbers in organism group 1 and 2 (see legend on figure). As such, squares with a large X-value and a low Y-value are expanded gene families in organism group 1, while squares with a large Y-Value and a low X-value represent expanded gene families in organism group 2. Squares situated around the diagonal can be considered not to be expanded.

All squares on the expansion plot are clickable and redirect to a table with the selected gene families. As such, it is easy for the user to have a closer look at the gene families of interest.
This tool can be considered to be complementary to the Gene Family Finder Tool.

• Parameters:
  • Maximum drawing size: Gene families with a too large copy number in either organisms group 1 or 2, are displayed on the outer border of the Expansion Plot. By increasing the maximum drawing size the range of axes is increased, leading to a decreasing number of squares on the border.
  • Normalize by number of selected species: When there is more than 1 species in either organism group 1 or 2, it becomes clear that comparing gene families purely on copy number introduces a bias towards the group with more organisms. Therefore the gene family copy number of the organism groups can be adapted so it averages over the number of species in that group.
  • Use only gene families where the selected species are all present: If selected, only those gene families, which have a representative gene of each organism of both groups, will be displayed. Otherwise a single representative gene from each group will suffice to include the gene family. Selection of this option will result in a smaller set of gene families.
  • Use only gene families specific to the selected species: If selected, only those gene families which have only representative genes from the selected organisms, will be displayed. Selection of this option will result in a smaller set of gene families.
• This tool can be found at Analyze → Expansion plot.

• View the phylogenetic tree of the homologous gene family.
• Using PhyD3 trees are visualized and several features can displayed (speciation/duplication nodes, intron/exon structures and InterPro domains). For more details, check the corresponding paper .
• Due to the editing of the multiple sequence alignment prior tree construction, some taxa showing too many gaps in the alignment or representing partial genes are discarded (cfr. 'Outlier/stripped gene information').
• The Tree explorer can be accessed through a gene family page.

• The Interactive Phylogenetics Module is meant to generate the phylogenetic tree of user-selected sequences.
• The user first inputs a seed gene or gene family identifier.
• A selection has to be made of sequences to be analyzed based on the BLAST hits of the query gene OR species-based selection based on the corresponding gene family; only one of the selection modes can be used at the same time. Also external sequences (either DNA/protein sequences) can optionally be inputted.
• The algorithm used for generation of the MSA can be either MUSCLE or MAFFT using automatic method detection. Next, the user can choose to perform no editing, removal of lowly conserved positions, filtering of partial sequences or both filtering and trimming. Finally, the phylogenetic tree construction has to be defined, which can be either the approximate maximum likelihood FastTree or the maximum likelihood methods PhyML, RaXML, or IQ-TREE. The latter will perform a test to detect the best fitting protein model from the following widely used models: JTT, LG, WAG, Blosum62, VT and Dayhoff. Thousand rounds of ultraparametric bootstrapping are run in IQ-TREE and the FreeRate model is used for rate heterogeneity across sites. All other methods use the WAG protein model in combination with 100 bootstraps and gamma approximation for modelling rate heterogeneity across sites.
• PhyD3 is used to visualize the generated phylogenetic tree. All intermediate and final files can be downloaded from the Files tab. All used commands and software versions can be displayed and finally detailed information about alignment construction and processing is visible in the Extra tab.
• The Tree explorer can be either accessed directly through Analyze → Interactive Phylogenetics Module or indirectly from a gene/gene family page.

• The Circle Plot reports all colinear regions within a single species using a circular representation. This plot uses nucleotide-based coordinates instead of genes (as the smallest unit).
• The data is the same as used for the WGDotplot (and thus generated using i-ADHoRe) while the tool is based on HTML5 canvas-drawing (with Javascript). This allows for direct interaction with the visualization:
  • Coloring options (either by Ks-value or by chromosome)
  • Selection of chromosomes, which is done by selecting chromosome/scaffolds in the section Chromosome display selection. Colinear regions that start/stop at the selected chromosome will appear/disappear as well.
  • Selection of colinear regions, which is done by selecting chromosome/scaffolds in the section Chromosome colinearity selection. When a chromosome is selected, then colinear regions starting/stopping in the chromosome will be displayed. When a chromosome is not selected, then colinear regions starting/stopping the chromosome will not be displayed. The associated figure shows for example the circleplot when all chromosomes (except 5) have not been selected.
• Other options include:
  • The visualization of colinear regions with other organisms on the outer border of the Circle Plot, by selecting the Add extra organisms option.
  • The mapping of (coding) gene density on the outer border of the Circle Plot, making it easier to identify regions on the chromosome with low coding potential, such as centromeres.
  • The mapping of genes with a specific Gene Ontology (GO) term or InterPro domain on the outer border of the Circle Plot. This can be used to identify whether certain genes are conserved within a colinear region.
• This tool can be found at Analyze → WGDotplot

• The Gene duplication analysis page displays for a given set of genes the fraction of block and tandem duplicates.
• For a gene set (e.g. gene families, genes associated with GO terms or InterPro domains) the fraction which is determined to be duplicated (by either a tandem duplication event or a block duplication event/WGD) is reported. This analysis is displayed in a bar-chart, with the various types of duplications indicated on the page, organized per species. This is useful for examining the mode of duplication responsible for the expansions of gene copy number within a set of genes.
• This tool can be reached through each gene family page, GO term page or InterPro page, through the summary of gene duplication types displayed below the pie-chart (with number copy per species) on each page.

• The Multiplicon view displays the aligned gene strings of a set of homologous segments.
• Colinear segments detected by i-ADHoRe are grouped into multiplicons. These are initially pairwise (level 2) but i-ADHoRe will iteratively go through the genomes adding, if available, extra homologous segments (profile search). Below the image a list is shown with all multiplicons detected using a profile based on the current multiplicon. These segments are aligned using i-ADHoRe's greedy graph aligner.
• The visualization is fully JavaScript-driven, and allows for a variety of interactive options:
  • Selection of species for which to display the colinear regions
  • Ordering of the colinear segments in the visualization
  • Whether or not to draw all genes, or only the colinear ones
• Additionally, by clicking on a gene a variety of extra information is displayed, with the necessary linkouts to allow the end-user to freely navigate the PLAZA platform to other entities of interest.
• This tool can be reached through the WGDotplot and the Skyline Plot.

• The Synteny plot reports the local gene organization for homologous genes within a family.
• Starting from a selected family the gene organization of all homologs of that family is reported. Strand information and different gene types are indicated by arrows and other symbols (see Legend), respectively, and genes belonging to the same gene family are coded by the same color.
• Functional annotation information from the gene family is always displayed, and can be easily compared to other genes/gene families by clicking on the genes in the plot.
• When hovering over a single gene, all genes of the same gene family within the same view
• A variety of options are available to the end-user to help with the analysis of the gene family in question :
  • The window size option makes it possible to change the number of genes around the locus from the selected gene family (5, 10 or 15 genes).
  • The strand orientation option can be used to draw all genes on the forward strand, or use the original gene orientation.
  • The syntenic regions are clustered by default by the PLAZA platform to place the most similar ones together. If required however, syntenic regions can also be clustered by species.
  • Both a species and clade selection option are available, allowing the end-user to narrow down the view in order not to be overwhelmed by the large amount of data available.
  • The end-user can set both the number of syntenic regions on a single page, as well as select the page to be displayed.
• This tool can be found at Analyze → Synteny plot

• Physical clustering of functionally related genes.
• Functional clusters of genes were detected using C-Hunter using all gene-GO annotations. C-Hunter was run with different settings (check settings here) and the results are stored as different experiments.
• The functional clustering visualization tool gives an overview of the location and content of each functional cluster on a chromosome-wide scale. Each cluster in the image is clickable and redirects to an overview page of the cluster, detailing the genes present in the cluster as well as their associated gene families.
• This tool can be found at Analyze → Functional clusters.

• Tool that allows users to visually inspect the genomes, with various features mapped onto the raw sequence.
• To browse the raw genomic sequence and visualize various features (e.g. gene models) users can use the HTML5 IGV.js genome browser.This genome browser has the following features:
  • Individual tracks can be rescaled or even hidden. This flexibility allows users to study the data they are interested in and hide everything else.
  • Currently only gene models and raw sequence data is viewable, but as more data will be added to the platform (e.g. cis-regulatory elements), these will become available in the genome browsers as well.
• This tool can be found on the organism pages. Alternatively a gene of interest can be visualized in the genome browser through the gene page (Toolbox → View → ...the gene in the Genome Browser ).