Bosque is a distributed software environment oriented to manage the computational resources involved in typical phylogenetic analyses. Bosque has been implemented as a client-server application where the server can execute installed phylogenetic programs (Phylip, PhyML, TreePuzzle, Muscle) and the client manages the results on a local relational database, although it can also execute phylogenetic programs locally, useful when no server is available. The client also performs the graphical visualisation and edition of trees and alignments, providing an environment for the analyses, from the integration of sequences to the printing of a final tree.
Network is used to reconstruct phylogenetic networks and trees, infer ancestral types and potential types, evolutionary branchings and variants, and to estimate datings. Network generates evolutionary trees and networks from genetic, linguistic, and other data. Network can then provide age estimates for any ancestor in the tree.
Mason is a read simulator software for Illumina, 454 and Sanger reads. Its features include position specific error rates and base quality values. For Illumina reads, we give a comprehensive analysis with empirical data for the error and quality model. For the other technologies, we use models from the literature. It has been written with performance in mind and can sample reads from large genomes.
EuGene is a gene redesign software. It allows opening and parsing genome files, loading genes into a workspace, and redesign the genes according to many redesign methodologies such as enhancing codon usage, codon context, GC content, hidden stop codons, repeated codons or nucleotides, harmonizing genes to other host species, avoiding deleterious sequences, among others. EuGene is free and auto-updates so you can always be up to the latest features and corrections.
FastPval is a two stage p-value computation software which compute the empirical p-value by two stage ranking strategy, it can produce very low P-value based on huge dataset. This fast and powerful tool takes advantage of a delicate cutoff which separate the exactly significant area. Compared to the traditional ranking method, Tspvc has a good time efficiency, lower memory consuming and tiny storage spaces with high accuracy.
MetaGenomeThreader, a software to predict genes, such as PCS’s (predicted coding sequences) in sequences of metagenome projects.
D.J. Schmitz-Hübsch and S. Kurtz.
MetaGenomeThreader: A software tool for predicting genes in DNA-sequences of metagenome projects.
In R. Daniel and W. Streit (Eds.), Metagenomics. Methods in Molecular Biology, 325–338, Humana Press, Totowa, NJ, ISBN 978-1-60761-822-5
GtEncseq, a compressed biosequence representation with many features.
TreeView is a simple program for displaying phylogenies on Apple Macintosh and Windows PCs.TreeView provides a simple way to view the contents of a NEXUS, PHYLIP, Hennig86, Clustal, or other format tree file. While PAUP and MacClade have excellent tree printing facilities, there may be times you just want to view the trees without having to load the data set they were generated from. The PHYLIP package contains tree drawing programs which offer a greater variety of trees than TreeView, but are somewhat clumsy to use. The forthcoming PAUP* for Windows does not have a graphical interface, hence TreeView allows you to create publication quality trees from PAUP files, either directly, or by generating graphics files for editing by other programs.
TreeView X is an open source program to display phylogenetic trees on Linux, Unix, Mac OS X, and Windows platforms