View phylogenetic tree
Author: N | 2025-04-25
Phylogenetic Tree View 1.5.0 APK download for Android. Import and view phylogenetic trees Phylogenetic reconstruction, and operations on phylogenetic trees. - GitHub - qiime2/q2-phylogeny: Phylogenetic reconstruction, and operations on phylogenetic trees. View all files.
Tree View: An application to display phylogenetic trees on
Scientists attempt to map the evolutionary pathways of all life on Earth. Many scientists build phylogenetic trees to illustrate evolutionary relationships.Structure of Phylogenetic TreesA phylogenetic tree can be read like a map of evolutionary history. Many phylogenetic trees have a single lineage at the base representing a common ancestor. Scientists call such trees rooted, which means there is a single ancestral lineage (typically drawn from the bottom or left) to which all organisms represented in the diagram relate. Notice in the rooted phylogenetic tree that the three domains—Bacteria, Archaea, and Eukarya—diverge from a single point and branch off. The small branch that plants and animals (including humans) occupy in this diagram shows how recent and miniscule these groups are compared with other organisms. Unrooted trees don’t show a common ancestor but do show relationships among species.Figure 2. Both of these phylogenetic trees shows the relationship of the three domains of life—Bacteria, Archaea, and Eukarya—but the (a) rooted tree attempts to identify when various species diverged from a common ancestor while the (b) unrooted tree does not. (credit a: modification of work by Eric Gaba)In a rooted tree, the branching indicates evolutionary relationships (Figure 3). The point where a split occurs, called a branch point, represents where a single lineage evolved into a distinct new one. A lineage that evolved early from the root and remains unbranched is called basal taxon. When two lineages stem from the same branch point, they are called sister taxa. A branch with more than two lineages is called a polytomy and serves to illustrate where scientists have not definitively determined all of the relationships. It is important to note that although sister taxa and polytomy do share an ancestor, it does not mean that the groups of organisms split or evolved from each other. Organisms in two taxa may have split apart at a specific branch point, but neither taxa gave rise to the other.Figure 3. The root of a phylogenetic tree indicates that an ancestral lineage gave rise to all organisms on the tree. A branch point indicates where two lineages diverged. A lineage that evolved early and remains unbranched is a basal taxon. When two lineages stem from the same branch point, they are sister taxa. A branch with more than two lineages is a polytomy.The diagrams above can serve as a pathway to understanding evolutionary history. The pathway can be traced from
view - View phylogenetic tree - MATLAB - MathWorks
The origin of life to any individual species by navigating through the evolutionary branches between the two points. Also, by starting with a single species and tracing back towards the “trunk” of the tree, one can discover that species’ ancestors, as well as where lineages share a common ancestry. In addition, the tree can be used to study entire groups of organisms.Another point to mention on phylogenetic tree structure is that rotation at branch points does not change the information. For example, if a branch point was rotated and the taxon order changed, this would not alter the information because the evolution of each taxon from the branch point was independent of the other.Many disciplines within the study of biology contribute to understanding how past and present life evolved over time; these disciplines together contribute to building, updating, and maintaining the “tree of life.” Information is used to organize and classify organisms based on evolutionary relationships in a scientific field called systematics. Data may be collected from fossils, from studying the structure of body parts or molecules used by an organism, and by DNA analysis. By combining data from many sources, scientists can put together the phylogeny of an organism; since phylogenetic trees are hypotheses, they will continue to change as new types of life are discovered and new information is learned.Video ReviewLimitations of Phylogenetic TreesIt may be easy to assume that more closely related organisms look more alike, and while this is often the case, it is not always true. If two closely related lineages evolved under significantly varied surroundings or after the evolution of a major new adaptation, it is possible for the two groups to appear more different than other groups that are not as closely related. For example, the phylogenetic tree in Figure 4 shows that lizards and rabbits both have amniotic eggs, whereas frogs do not; yet lizards and frogs appear more similar than lizards and rabbits.Figure 4. This ladder-like phylogenetic tree of vertebrates is rooted by an organism that lacked a vertebral column. At each branch point, organisms with different characters are placed in different groups based on the characteristics they share.Another aspect of phylogenetic trees is that, unless otherwise indicated, the branches do not account for length of time, only the evolutionary order. In other words, the length of a branch does not typically mean more time passed, nor does a short branchPhylogenetic trees for streptomycete. The phylogenetic tree is
(HCCA). Calibration of the spectrometer was performed using Escherichia coli DH5α, and a non-inoculated matrix served as a negative control. To ensure data reliability, the sample was analyzed in triplicate and the identification confidence was evaluated based on score thresholds, with scores ≥1.9 considered low confidence and scores Streptomyces genus. 2.4. DNA Extraction, 16SrRNA Gene Sequencing and Phylogenetic AnalysisThe genomic DNA of the ACT158 strain was extracted as described by Kieser et al. [22]. The 16S rRNA gene was amplified by PCR using a pair of the universal primers Fd1 (5′ AGAGTTTGATCCTGGCTCAG) and rP2 (5′-AAGGAGGTGATCCAGCC) [23]. Amplified product was sequenced and homology searches were conducted by comparing sequences with those in public databases (NCBI) using the Basic Local Alignment Search Tool (BLAST), v. 2.16.0 and EzBioCloud database ( accessed on 10 January 2025) [24]. Phylogenetic analyses were performed using MEGA software version 11, with sequences aligned against neighboring nucleotide sequences using CLUSTALW [25]. The phylogenetic tree was constructed using the neighbor-joining (NJ) method, and the topologies were evaluated through bootstrap sampling based on 1000 replicates. 2.5. Antimicrobial Testing Activity of Streptomyces sp. ACT158The antibacterial activity of Streptomyces sp. ACT158 was evaluated using the agar diffusion method as described by Benhadj et al. [8]. Mycelium plugs (7 mm) deposited onto LB (Luria and Bertani) plates inoculated with bacterial indicator strains (Table S1) at an optical density of 0.04 and the activity was assessed over 3, 7, 10, 14, 17, and 21 days. Two culture media, ISP2 and glycerol yeast extract agar. Phylogenetic Tree View 1.5.0 APK download for Android. Import and view phylogenetic trees Phylogenetic reconstruction, and operations on phylogenetic trees. - GitHub - qiime2/q2-phylogeny: Phylogenetic reconstruction, and operations on phylogenetic trees. View all files.Phylogenetic tree viewing software - ResearchGate
Read and analyze a phylogenetic tree that documents evolutionary relationshipsIn scientific terms, the evolutionary history and relationship of an organism or group of organisms is called phylogeny. Phylogeny describes the relationships of an organism, such as from which organisms it is thought to have evolved, to which species it is most closely related, and so forth. Phylogenetic relationships provide information on shared ancestry but not necessarily on how organisms are similar or different.Learning ObjectivesIdentify how and why scientists classify the organisms on earthDifferentiate between types of phylogenetic trees and what their structure tells usIdentify some limitations of phylogenetic treesRelate the taxonomic classification system and binomial nomenclatureScientific ClassificationFigure 1. Only a few of the more than one million known species of insects are represented in this beetle collection. Beetles are a major subgroup of insects. They make up about 40 percent of all insect species and about 25 percent of all known species of organisms.Why do biologists classify organisms? The major reason is to make sense of the incredible diversity of life on Earth. Scientists have identified millions of different species of organisms. Among animals, the most diverse group of organisms is the insects. More than one million different species of insects have already been described. An estimated nine million insect species have yet to be identified. A tiny fraction of insect species is shown in the beetle collection in Figure 1.As diverse as insects are, there may be even more species of bacteria, another major group of organisms. Clearly, there is a need to organize the tremendous diversity of life. Classification allows scientists to organize and better understand the basic similarities and differences among organisms. This knowledge is necessary to understand the present diversity and the past evolutionary history of life on Earth.Phylogenetic TreesScientists use a tool called a phylogenetic tree to show the evolutionary pathways and connections among organisms. A phylogenetic tree is a diagram used to reflect evolutionary relationships among organisms or groups of organisms. Scientists consider phylogenetic trees to be a hypothesis of the evolutionary past since one cannot go back to confirm the proposed relationships. In other words, a “tree of life” can be constructed to illustrate when different organisms evolved and to show the relationships among different organisms (Figure 2).Each group of organisms went through its own evolutionary journey, called its phylogeny. Each organism shares relatedness with others, and based on morphologic and genetic evidence,Phylogenetic Tree View on the App Store
Geneious Prime provides inbuilt algorithms for Neighbour-joining (Saitou & Nei 1987) and UPGMA (Mitchener & Sokal 1957) methods of tree reconstruction, which are suitable for preliminary investigation of relationships between newly acquired sequences. For more sophisticated methods of phylogenetic reconstruction such as Maximum Likelihood and Bayesian MCMC, external plugins for specialist software are available. These can be downloaded from the plugins page on our website or within Geneious by going to Plugins under the Tools menu.Phylogenetic tree representationA phylogenetic tree describes the evolutionary relationships amongst a set of sequences. They have a few commonly associated terms that are depicted in the figure below: Branch length. A measure of the amount of divergence between two nodes in the tree. Branch lengths are usually expressed in units of substitutions per site of the sequence alignment.Nodes or internal nodes of a tree represent the inferred common ancestors of the sequences that are grouped under them.Tips or leaves of a tree represent the sequences used to construct the tree.Taxonomic units. These can be species, genes or individuals associated with the tips of the tree.A phylogenetic tree can be rooted or unrooted. A rooted tree consists of a root, or the common ancestor for all the taxonomic units of the tree. An unrooted tree is one that does not show the position of the root. An unrooted tree can be rooted by adding an outgroup (a species that is distantly related to all the taxonomic units in the tree).For information on viewing and formatting trees in Geneious, see Viewing and Formatting Trees. Tree building in Geneious PrimeTo build a tree, select an alignment or a set of related sequences (all DNA or all protein) in the Document table and click the Tree icon or choose this option from the Tools menu. If you are building a simple tree (Neigbour joining or UPGMA) using the Geneious tree builder, the tree can be built directly from a set of unaligned sequences, as the alignment will be built as part of the tree-building process. For more advanced trees, or if you wish to bootstrap your trees you must build an alignment first and use that as input for your tree. You can also select an existing tree document (which contains an alignment) and build another tree from that, as the alignment will simply be extracted from the existing tree and used build the new tree.The following options are available in the tree-building dialog for the Geneious tree builder. For more information on these options see Tree building methods and models.Exclude masked sites. Excludes sites containing Masked annotations from the analysis without permanently removing them from your alignment. See Using alignment masks for further information.Genetic distance model. This lets the user choose the kind of substitution model used to estimate branch lengths. If you are building a tree from DNA sequences you have the choices "Jukes Cantor", "HKY" and "Tamura Nei". If you are building a tree from amino acid sequences you only have the option of "Jukes Cantor"Phylogenetic tree view - The Botanist in the Kitchen
Now when you’re asked to define a tree, you should be able to give the basic pointers about its nature like:Woody: Stems and roots show secondary growth.Perennial: Live for a good number of years (renew growth year after year). Although there are deciduous trees too that shed their leaves every season. So, when asked how do trees grow, there’s no one specific way, but generally, trees are perennial.Profusely branched: Branching happens high above the ground level and a certain level of canopy formation is there!Ubiquitous in nature: Spread around the globe across different ecosystems and habitats.Multifunctional: Produce oxygen, prevent soil erosion, contribute to ecosystem stability, yield products of importance to life (food, clothing, shelter, ecosystem services, etc.)Division of Kingdom Plantae containing trees: Pteridophytes, Gymnosperms, Angiosperms.An important point to note when we try to understand the meaning of a tree is that “tree is not a separate taxon”; meaning it’s not a specific taxonomic group per se. It’s just a category of plants based on some distinguishing features.1. Members of various different taxa (Pteridophytes, Gymnosperms, Angiosperms) at the Division level can be examples of trees.2. Members of various different taxa (Cyatheaceae, Pinaceae, Rutaceae) at the Family level can be examples of trees.3. But trees aren’t a separate taxon themselves!To learn more about “what a taxon is?”, read our article on TAXON here.Classification of TreesJust like there’s no one fixed, standout way to tell what a tree is or what a tree means, there’s no one definite way to define a group of trees. While some scientists prefer to sort them phylogenetically, others prefer to categorize them based on morphological and ecological habitat preferences. Let’s look at each of them one by one and decipher the diversity.A. Phylogenetic classificationAccording to the phylogenetic concept, different types of trees can be divided into 3. Phylogenetic Tree View 1.5.0 APK download for Android. Import and view phylogenetic treesComments
Scientists attempt to map the evolutionary pathways of all life on Earth. Many scientists build phylogenetic trees to illustrate evolutionary relationships.Structure of Phylogenetic TreesA phylogenetic tree can be read like a map of evolutionary history. Many phylogenetic trees have a single lineage at the base representing a common ancestor. Scientists call such trees rooted, which means there is a single ancestral lineage (typically drawn from the bottom or left) to which all organisms represented in the diagram relate. Notice in the rooted phylogenetic tree that the three domains—Bacteria, Archaea, and Eukarya—diverge from a single point and branch off. The small branch that plants and animals (including humans) occupy in this diagram shows how recent and miniscule these groups are compared with other organisms. Unrooted trees don’t show a common ancestor but do show relationships among species.Figure 2. Both of these phylogenetic trees shows the relationship of the three domains of life—Bacteria, Archaea, and Eukarya—but the (a) rooted tree attempts to identify when various species diverged from a common ancestor while the (b) unrooted tree does not. (credit a: modification of work by Eric Gaba)In a rooted tree, the branching indicates evolutionary relationships (Figure 3). The point where a split occurs, called a branch point, represents where a single lineage evolved into a distinct new one. A lineage that evolved early from the root and remains unbranched is called basal taxon. When two lineages stem from the same branch point, they are called sister taxa. A branch with more than two lineages is called a polytomy and serves to illustrate where scientists have not definitively determined all of the relationships. It is important to note that although sister taxa and polytomy do share an ancestor, it does not mean that the groups of organisms split or evolved from each other. Organisms in two taxa may have split apart at a specific branch point, but neither taxa gave rise to the other.Figure 3. The root of a phylogenetic tree indicates that an ancestral lineage gave rise to all organisms on the tree. A branch point indicates where two lineages diverged. A lineage that evolved early and remains unbranched is a basal taxon. When two lineages stem from the same branch point, they are sister taxa. A branch with more than two lineages is a polytomy.The diagrams above can serve as a pathway to understanding evolutionary history. The pathway can be traced from
2025-04-16The origin of life to any individual species by navigating through the evolutionary branches between the two points. Also, by starting with a single species and tracing back towards the “trunk” of the tree, one can discover that species’ ancestors, as well as where lineages share a common ancestry. In addition, the tree can be used to study entire groups of organisms.Another point to mention on phylogenetic tree structure is that rotation at branch points does not change the information. For example, if a branch point was rotated and the taxon order changed, this would not alter the information because the evolution of each taxon from the branch point was independent of the other.Many disciplines within the study of biology contribute to understanding how past and present life evolved over time; these disciplines together contribute to building, updating, and maintaining the “tree of life.” Information is used to organize and classify organisms based on evolutionary relationships in a scientific field called systematics. Data may be collected from fossils, from studying the structure of body parts or molecules used by an organism, and by DNA analysis. By combining data from many sources, scientists can put together the phylogeny of an organism; since phylogenetic trees are hypotheses, they will continue to change as new types of life are discovered and new information is learned.Video ReviewLimitations of Phylogenetic TreesIt may be easy to assume that more closely related organisms look more alike, and while this is often the case, it is not always true. If two closely related lineages evolved under significantly varied surroundings or after the evolution of a major new adaptation, it is possible for the two groups to appear more different than other groups that are not as closely related. For example, the phylogenetic tree in Figure 4 shows that lizards and rabbits both have amniotic eggs, whereas frogs do not; yet lizards and frogs appear more similar than lizards and rabbits.Figure 4. This ladder-like phylogenetic tree of vertebrates is rooted by an organism that lacked a vertebral column. At each branch point, organisms with different characters are placed in different groups based on the characteristics they share.Another aspect of phylogenetic trees is that, unless otherwise indicated, the branches do not account for length of time, only the evolutionary order. In other words, the length of a branch does not typically mean more time passed, nor does a short branch
2025-04-18Read and analyze a phylogenetic tree that documents evolutionary relationshipsIn scientific terms, the evolutionary history and relationship of an organism or group of organisms is called phylogeny. Phylogeny describes the relationships of an organism, such as from which organisms it is thought to have evolved, to which species it is most closely related, and so forth. Phylogenetic relationships provide information on shared ancestry but not necessarily on how organisms are similar or different.Learning ObjectivesIdentify how and why scientists classify the organisms on earthDifferentiate between types of phylogenetic trees and what their structure tells usIdentify some limitations of phylogenetic treesRelate the taxonomic classification system and binomial nomenclatureScientific ClassificationFigure 1. Only a few of the more than one million known species of insects are represented in this beetle collection. Beetles are a major subgroup of insects. They make up about 40 percent of all insect species and about 25 percent of all known species of organisms.Why do biologists classify organisms? The major reason is to make sense of the incredible diversity of life on Earth. Scientists have identified millions of different species of organisms. Among animals, the most diverse group of organisms is the insects. More than one million different species of insects have already been described. An estimated nine million insect species have yet to be identified. A tiny fraction of insect species is shown in the beetle collection in Figure 1.As diverse as insects are, there may be even more species of bacteria, another major group of organisms. Clearly, there is a need to organize the tremendous diversity of life. Classification allows scientists to organize and better understand the basic similarities and differences among organisms. This knowledge is necessary to understand the present diversity and the past evolutionary history of life on Earth.Phylogenetic TreesScientists use a tool called a phylogenetic tree to show the evolutionary pathways and connections among organisms. A phylogenetic tree is a diagram used to reflect evolutionary relationships among organisms or groups of organisms. Scientists consider phylogenetic trees to be a hypothesis of the evolutionary past since one cannot go back to confirm the proposed relationships. In other words, a “tree of life” can be constructed to illustrate when different organisms evolved and to show the relationships among different organisms (Figure 2).Each group of organisms went through its own evolutionary journey, called its phylogeny. Each organism shares relatedness with others, and based on morphologic and genetic evidence,
2025-04-17Geneious Prime provides inbuilt algorithms for Neighbour-joining (Saitou & Nei 1987) and UPGMA (Mitchener & Sokal 1957) methods of tree reconstruction, which are suitable for preliminary investigation of relationships between newly acquired sequences. For more sophisticated methods of phylogenetic reconstruction such as Maximum Likelihood and Bayesian MCMC, external plugins for specialist software are available. These can be downloaded from the plugins page on our website or within Geneious by going to Plugins under the Tools menu.Phylogenetic tree representationA phylogenetic tree describes the evolutionary relationships amongst a set of sequences. They have a few commonly associated terms that are depicted in the figure below: Branch length. A measure of the amount of divergence between two nodes in the tree. Branch lengths are usually expressed in units of substitutions per site of the sequence alignment.Nodes or internal nodes of a tree represent the inferred common ancestors of the sequences that are grouped under them.Tips or leaves of a tree represent the sequences used to construct the tree.Taxonomic units. These can be species, genes or individuals associated with the tips of the tree.A phylogenetic tree can be rooted or unrooted. A rooted tree consists of a root, or the common ancestor for all the taxonomic units of the tree. An unrooted tree is one that does not show the position of the root. An unrooted tree can be rooted by adding an outgroup (a species that is distantly related to all the taxonomic units in the tree).For information on viewing and formatting trees in Geneious, see Viewing and Formatting Trees. Tree building in Geneious PrimeTo build a tree, select an alignment or a set of related sequences (all DNA or all protein) in the Document table and click the Tree icon or choose this option from the Tools menu. If you are building a simple tree (Neigbour joining or UPGMA) using the Geneious tree builder, the tree can be built directly from a set of unaligned sequences, as the alignment will be built as part of the tree-building process. For more advanced trees, or if you wish to bootstrap your trees you must build an alignment first and use that as input for your tree. You can also select an existing tree document (which contains an alignment) and build another tree from that, as the alignment will simply be extracted from the existing tree and used build the new tree.The following options are available in the tree-building dialog for the Geneious tree builder. For more information on these options see Tree building methods and models.Exclude masked sites. Excludes sites containing Masked annotations from the analysis without permanently removing them from your alignment. See Using alignment masks for further information.Genetic distance model. This lets the user choose the kind of substitution model used to estimate branch lengths. If you are building a tree from DNA sequences you have the choices "Jukes Cantor", "HKY" and "Tamura Nei". If you are building a tree from amino acid sequences you only have the option of "Jukes Cantor"
2025-03-29Pairwise distances (i.e., gaps are not treated as a 21st amino acid state).Jukes-CantorThis is the simplest substitution model. It assumes that all amino acids have the same equilibrium base frequency, i.e., each amino acid occurs with a frequency of 0.05 in protein sequences. This model also assumes that all amino acid substitutions occur at equal rates.If the proportion of non-gap, non-ambiguous sites that are mismatched between the sequences is given as $p$, the formula for computing the distance between the sequences is:d = -19/20 * log(1 - 20/19 * p)Under Jukes-Cantor the number of substitutions is assumed to be Poisson distributed with a rate of 20/19u, i.e., the probability of no substitutions at a given site over a branch of length ut is e-20/19ut.Technically, Jukes-Cantor for amino acid sequences is the Neyman model (Neyman 1971) with 20 states.Advanced Tree Building methodsOther plugins are available for running maximum likelihood or Bayesian phylogenetic analyses in Geneious, including MrBayes, PhyML, RAxML, FastTree, and PAUP*. These can be downloaded from the plugins page on our website or within Geneious by going to Plugins under the Tools menu. For more information on running these programs, please consult the user manual for the source software.Resampling - Bootstrapping and jackknifingResampling is a statistical technique where a procedure (such as phylogenetic tree building) is repeated on a series of datasets generated by sampling from one original dataset. The results of analyzing the sampled datasets are then combined to generate summary information about the original dataset.In the context of tree building, resampling involves generating a series of sequence alignments by sampling columns from the original sequence alignment. Each of these alignments (known as pseudoreplicates) is then used to build an individual phylogenetic tree. A consensus tree can then be constructed by combining information from the set of generated trees or the topologies that occur can be sorted by their frequency (see below).To resample a tree by bootstrapping or jackknifing with the Geneious Tree Builder, tick Resample Tree under the Consensus Tree Options and choose the method and number of replicates you want to perform. Bootstrapping is the statistical method of resampling with replacement. To apply bootstrapping in the context of tree building, each pseudo-replicate is constructed by randomly sampling columns of the original alignment with replacement until an alignment of the same size is obtained (see Felsenstein 1985).Jackknifing is a statistical method of numerical resampling based on deleting a portion of the original observations for each pseudo-replicate. A 50% jackknife randomly deletes half of the columns from the alignment to create each pseudo-replicate.Consensus treesA consensus tree provides an estimate for the level of support for each clade in the final tree. It is built by combining clades which occurred in at least a certain percentage of the resampled trees. This percentage is called the consensus support threshold. A 100% support threshold results in a Strict consensus tree which is a tree where the included clades are those that are present in all the trees of the original set. A
2025-04-21CAFESoftware for Computational Analysis of gene Family EvolutionThe purpose of CAFE is to analyze changes in gene family size in a way thataccounts for phylogenetic history and provides a statistical foundation forevolutionary inferences. The program uses a birth and death process to model genegain and loss across a user-specified phylogenetic tree. The distribution of familysizes generated under this model can provide a basis for assessing the significanceof the observed family size differences among taxa. to v4.2.1 is the latest in a regular series of releases to the CAFE application. Themanual and various tutorials may be viewed on the website ( . This document describes how todownload and use CAFE v4.2.1.UseThe necessary inputs for CAFE v4.2.1 are:a data file containing gene family sizes for the taxa included in thephylogenetic treea Newick formatted phylogenetic tree, including branch lengthsFrom the inputs above, CAFE v4.2.1 will compute:the maximum likelihood value of the birth & death parameter, λ (or ofseparate birth and death parameters (λ and μ, respectively), over the wholetree or for user-specified subsets of branches in the treeancestral states of gene family sizes for each node in the phylogenetic treep-values for each gene family describing the likelihood of the observed sizesgiven average rates of gain and lossaverage gene family expansion along each branch in the treenumbers of gene families with expansions, contractions, or no changealong each branch in the treeInstallRun "configure" and "make" from the home directory. The only result is the "cafe"executable in the release directory. This file should be copied to a convenientlocation.HistoryCAFE v3.0 was a major update to CAFE v2.1. Major updates in 3.0 included: 1) the ability to correctfor genome assembly and annotation error when analyzing gene family evolutionusing the errormodel command. 2) The ability to estimate separate birth (λ) anddeath (μ) rates using the lambdamu command. 3) The ability to estimate error inan input data set with iterative use of the errormodel command using theaccompanying python script caferror.py. This version also included the addition of therootdist command to give the user more control over simulations.CAFE v4.0 was the first release in a regular series of releases in order to makeCAFE easier and more user-friendly, in addition to adding features and fixing bugs.
2025-04-24