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SPIDIR / Species Informed Distance-based Reconstruction
Reconstructs gene-tree by using learning gene- and species-specific substitution rates across multiple complete genomes. SPIDIR achieves significantly higher accuracy, addresses the species-level heterotachy and enables studies of gene evolution in the context of species evolution. It uses a generative model of gene-tree evolution to calculate the likelihood of a phylogeny. The tool can be viewed as specifying a prior probability on gene-tree branch lengths, which could replace the uniform branch length prior.
P4P / Peptidomes for Phylogenies
Enables the in silico inference of bacterial taxonomy through the analysis of peptidomes. The P4P methodology uses whole genome data and in silico protein digestion to infer bacterial taxonomy, namely at the species and subspecies levels. The principal purpose is to generate a valid and manageable list of peptides that are potentially specific to each strain. This tool can also support accurate phylogenetic reconstruction for conventionally challenging groups of organisms.
Provides a git-based data store for archiving and curating phylogenetic estimates of species relationships. By incorporating curation into the data storage, Phylesystem have lowered the activation cost of entering data into an archive while also allowing continued curation, whether by the original authors or researchers interested in re-using these data, to improve the associated metadata. Phylesystem is part of The Open Tree of Life project and allows to complement systems by storing phylogenetic statements and associated metadata in a consistent format while retaining the history of edits that were made to the data themselves.
Computes the triplet and quartet distances between general rooted or unrooted trees, respectively. The tqDist program is based on algorithms with running time O(n log n) for the triplet distance calculation and O(d.n log n) for the quartet distance calculation, where n is the number of leaves in the trees and d is the degree of the tree with minimum degree. The software package is carefully implemented in C++, and interfaces for scripting in Python (via the module pyTQDist) and in R (via the package rtqdist) are also provided.
PREQUAL / PREalignment QUALity filtering
Allows automated and high-throughput detection of nonhomologous regions. PREQUAL is a program for pre-alignment quality filtering. It uses a probabilistic model to test evidence of homology between amino acid residues in pairs of unaligned sequences, and residues showing no statistical evidence of homology are filtered. Given a parameterized pair hidden Markov model (pairHMM), it calculates the posterior probability (PP) of a character being related to a character from another sequence.
SPIMAP / Species Informed Maximum A Posteriori Gene Tree Reconstruction
Provides a phylogenetic reconstruction method specifically designed for reconstructing gene trees in the case of a known species tree. SPIMAP uses a Bayesian framework to model sequence evolution, gene duplication, loss, and substitution rate variation, thus incorporating many disparate types of information in a principled way. This method models rate variation that is correlated across all branches of the tree (gene-specific rate) as well as rates specific to each species lineage (species-specific rates). When both these effects are modeled, the result is a more informative prior which leads to increased reconstruction accuracy.
Assists is carrying out and teaching meta-analysis in Ecology and Evolutionary biology (E&E). OpenMEE was developed to make advanced methods for statistical research synthesis, based on best practices, available without cost to the scientific community by providing an intuitive graphical user interface (GUI) to the diverse and growing statistical functionalities of the R ecosystem. Its interface also guides users to build appropriate synthesis models that provide high-quality analyses for the most common and important ecological questions.
Allows to work about the history of recombination events that affected a given sample of bacterial genomes. ClonalOrigin run on as comparative analysis of sequences of a sample of bacterial genomes and enables to reconstruct the recombination events that have taken place in their ancestry. It contains an algorithm which permits to perform inference under this model from sequence data alignments and demonstrates that through parallelization, the inference is conceivable for whole-genome alignments.
SCOTTI / Structured COalescent Transmission Tree Inference
Models each host as a distinct population, and transmissions between hosts as migration events. This phylogenetic software can (i) infer transmission events, (ii) account for the uncertainty associated with the possible presence of non-sampled hosts and (iii) use data from multiple samples of the same host. SCOTTI not only accounts for diversity and evolution within a host, but also for other sources of bias, namely non-sampled hosts and multiple infections of the same host. SCOTTI addresses the urgent need for software to analyse genomic and epidemiological data while accommodating for incomplete or patchy host sampling, mixed infections, and within-host variation. For these reasons, this method can help to reconstruct transmission histories in a broad range of outbreaks, both bacterial and viral.
MitoPhAST / Mitogenome Phylogenetic Analysis of Sequences Tool
Identifies annotated protein-coding gene features, generates a maximum likelihood phylogenetic tree and reports various mitochondrial genes and sequence information in a table format. The recovered phylogenetic trees using both Bayesian and ML methods support the results of studies using fragments of mtDNA and nuclear markers and other smaller-scale studies using whole mitogenomes. In comparison to the fragment-based phylogenies, nodal support values are generally higher despite reduced taxon sampling suggesting there is value in utilising more fully mitogenomic data.
STAG-CNS / Suffix Tree Arbitrary Gene number: Conserved Noncoding Sequence
Characterizes loss of conserved noncoding sequences associated with retained duplicate genes from the ancient maize polyploidy. STAG-CNS integrates data from the promoters of conserved orthologous genes in three or more species simultaneously. It can also be used to identify differences in the loss or retention of conserved non-coding sequences between duplicated genes. It can be employs to identify even smaller regions of conserved sequence within gene promoters with acceptable false discovery proportions.
Phylo-HMGP / Phylogenetic Hidden Markov Gaussian Processes
Allows genome-wide state estimation based on multivariate features from different species, using functional genomic signals. Phylo-HMGP is a continuous-trait probabilistic model that incorporates the evolutionary affinity among multiple species into the hidden Markov model (HMM). It thus exploits both temporal dependencies across species in the context of evolution, and spatial dependencies along the genome in a continuous-trait model. The software can be applied to different types of functional genomic signals.
Provides users a solution for measuring and analyzing compositional change for occurrence data using zeta diversity. Zetadiv is a program that permits several types of analysis on zeta diversity: (1) the analysis of zeta diversity; (2) the analysis of the distance decay of zeta diversity; or (3) the analysis of the hierarchical scaling of zeta diversity. It also includes features for computing zeta-diversity for a specific number of assemblages and for a range of numbers of assemblages.
HiMAP / Highly Multiplexed Amplicon-based Phylogenomics
Produces phylogenomic datasets using highly multiplexed amplicon sequencing. HiMAP employs amplicon sequencing based on highly multiplexed polymerase chain reaction (PCR) to generate its datasets. It provides features for locus selection, primer design, target amplification, sequencing, and post-sequencing data processing and analysis. The method requires minimal hands-on time at the bench, and data can be processed rapidly for consensus calls that permits avoiding read mapping or assembly.
Quartet Index
Provides a set of scripts performing several computations related to the Quartet Index. Quartet Index is defined as the sum, over all 4-tuples of different leaves of the tree, of a value that quantifies the symmetry of the joint evolution of the species they represent. It can be computed in linear time and its expected value and variance can be explicitly computed on any probabilistic model of phylogenetic trees satisfying two natural conditions: independence under relabeling and sampling consistency.
Enables detection of all orthologs that share a given evolutionary context. CLfinder-OrthNet identifies co-linearity (CL) in the arrangement of orthologous loci among multiple genomes and builds networks of orthologs to encode and visualize all evolutionary events, such as gene duplication, deletion, and transposition, in each orthologs group. It detects multiple forms of gene-level structural variation, including tandem duplications, deletions, transpositions, and also combinations of them.
STS / Suffix Tree Searcher
Allows the analysis of large numbers of unaligned long DNA sequences through the application of disk-based partitioned suffix trees (based on MGB’s DiGeST). STS is designed as an easy-to-use tool to index, search, and analyze very large DNA sequence datasets. Accordingly, the program is accessed through a Java Web Start link on a web page, which automatically installs or updates the program files for the user. Results are presented in tabular form, can be sorted based on multiple criteria, and are easily integrated into subsequent queries with a mouse click, providing for a natural analysis workflow. In addition, since the initial construction of suffix trees is computationally expensive, STS allows the user to load previously constructed suffix trees for analysis. Thus, once the suffix tree forest has been constructed for a given data set, future analyses can be run much more quickly by skipping the most time-consuming step.
Allows users to import trees with bootstraps and branch lengths and then root the tree, collapse the tree, and measure the length and other attributes. TreeCollapseCL is a Java program that can (1) rooted or re-rooted the tree to the outgroup specified by the user, (2) collapse all nodes with bootstrap values below the threshold provided by the user to polytomies, and (3) calculate the length from each leaf to the node above the root node as well as the average bootstrap value for each leaf.
FGF / Fishing Gene Family
Integrates homologous search and evolutionary analysis. FGF is a web server that uses protein sequences as bait for fishing gene families and extracting related information. It permits to visualize the chromosomal position of the duplications, the exon–intron structure and construct a phylogenetic tree based on a distance matrix. It deciphers not only the members of a gene family, but also their evolutionary relationships and helps in deducing the fate of the duplications.
Allows exploration of a range of pre-defined phylo-grammars and provides tools for visualization of user’s phylo-grammars. xREI is a web server that provides a method for visualizing phylo-grammars developed within the xrate framework. The software handles xrate grammars and stockholm alignments with defined phylogenetic trees. It can produce state transition graphs and substitution rate matrices for the grammar, and also provide training and alignment annotation functions.
SESAM / Spatially Explicit Species Assemblage Modelling
Assists in predicting spatio-temporal patterns of species assemblages. SESAM integrates two approaches: (i) macroecological modelling (MEM) approach that focuses directly on realized properties of species assemblages, and (ii) stacked species distribution modelling (S-SDM) approach that starts with constituent species to approximate the properties of assemblages. It uses relevant designations of initial species source pools for modelling, macroecological variables, and ecological assembly rules.
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Offers a public knowledge-base for information on the tree-of-life and its evolutionary timescale. TimeTree is a web-based resource for researchers and educators from all fields of science to assist in the discovery of patterns and the formulation of hypotheses, or simply to learn about the timetree of life. The home page describes the database and presents a choice of two user-query forms: finding the divergence of two taxa, and finding all time estimates from a particular author. The current version contains timetrees reported from molecular clock analyses in 910 published studies and 17 341 species that span the diversity of life. TimeTree interprets complex and hierarchical data from these studies for each user query, which can be launched using an iPhone application, in addition to the website.
PANDIT / Protein and Associated Nucleotide Domains with Inferred Trees
Assists researchers to investigate molecular evolutionary phenomena and to develop phylogenetic and comparative genomic methodology. PANDIT provides a set of aligned protein coding sequences, both at the DNA and amino acid level. It offers estimation of the evolutionary trees describing the relationship between these sequences. The database allows users to quickly and efficiently produce datasets relevant for their needs.
DED / Database of Evolutionary Distances
Contains sequence information from several vertebrate species clustered into homology groups. DED is an online resource for gene function assignment, molecular phylogenetic studies, search for lateral gene transfer, reconstruction of identification of biochemical pathways in poorly characterized organisms and sequence evolution patterns. It also includes multiple sequence alignments for both protein and nucleotide sequences along with the phylogenetic trees and graphical representation of sequence relationships within a homology group.
Provides evolutionary models for all genomic components of fully sequenced bacterial genomes describing the pattern of common ancestry observed among sequences. GeneTrees is a phylogenomics analysis platform that presents integrated visualization of phylogenetic models with their underlying sequence data. The database is structured as a list of taxa (species or within-species variants such as strains) using the GenBank taxonomy, the complete set of protein sequences annotated for these genomes and a set of homology models.
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