Provides access to a set of parallel tree inference and multiple sequence alignment codes run on large computational resources. CIPRES Science Gateway is able to upload a dataset, configure a job run using a particular community code, run that job on a multicore compute cluster, and retrieve the results. Additionally, users can submit and run multiple jobs simultaneously.
Allows users to analyze molecular sequences. The Phylemon interface can be used by experts and non-expert users. It contains several types of features: (1) it allows users to design and save phylogenetic pipelines to be used over multiple genes; (2) it makes possible evolutionary analyses, format conversion, file storage and edition of results; and (3) it suggests further analyses, thereby guiding the users through the web server.
Produces multiple alignments and trees from genomic data. Hal is a phylogenetic pipeline. The alignments can be produced by a choice of four alignment programs and analyzed by a variety of phylogenetic programs. The Hal pipeline connects the programs BLASTP, MCL, user specified alignment programs, GBlocks, ProtTest and user specified phylogenetic programs to produce species trees.
Allows construction of matrices for phylogenomic analyses. Agalma is an automated phylogenomics workflow that conducts complete phylogenomic analyses, from raw sequence reads to preliminary phylogenetic trees, with a small number of high-level commands. The software enables fully reproducible phylogenomic studies. The method called treeinform, which uses phylogenetic information to identify misassigned transcripts and reassign them to the same gene, is included in the software.
An easy way for ecologists to make realistic, tenable phylogenies. With phyloGenerator, you can download real DNA sequence data for your species of interest, and then generate a calibrated phylogeny using a defensible constraint tree. Your phylogeny may not be 'correct', but it will have branch lengths based on DNA data and its topology will be safe. It'll be a 'real' phylogeny, not a best-guess from taxonomy filled with polytomies. You don't need to have an advanced knowledge of phylogenetics to use phyloGenerator. Just download the program, follow the guide, and you can build a phylogeny in minutes.
Performs phylogenetics analyses on trees and sequences. phyx provides a collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects (alignments, trees and Markov Chain Monte Carlo (MCMC) logs). Modelled after Unix/GNU/Linux command line tools, individual programs perform a single task and operate on standard I/O streams that can be piped to quickly and easily form complex analytical pipelines. Because of the stream-centric paradigm, memory requirements are minimized (often only a single tree or sequence in memory at any instance), and hence phyx is capable of efficiently processing very large datasets.
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.