Bosque Publisher's description
Bosque is a distributed software environment oriented to manage the computational resources involved in typical phylogenetic analyses.
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.
One important feature of Bosque is that it allows multiple users to interact through the server, by talking on public channels and by sharing phylogenetic resources, such as sequences, trees, alignments, etc.
Bosque works under the following concepts:
* Tree Project. Bosque define a "tree project" as a group which consist of: 1) a set of sequences, 2) a posible alignment for these sequences and 3) a set of trees out of the previous alingment. A tree project is showed, within Bosque, on a special window called (guess..) Tree Window. A tree window then has at least two tabs: a sequence tab, an alignment tab and zero o more tree tabs. This is particularly useful when you want to construct different trees using different methods (maximum likelihood, distance, etc) but from the same data set, so you can confront analyses of the same data. In the, hopefully, near future we will provide a way to compute the consense tree out of the different trees you may have on a tree window.
* Phylogenetic Local Database. Instead of having lots of external files, on different formats, containing your phylogentic data, Bosque works with a local relational database, composed of differnt tables, which help to an efficient management of all the data. Sequences, alignments and trees are all saved on the local database, so you can start to forget words like: "newick", "nexus", "fasta", "gb", etc. This also has the advantage that allows you to keep your data well organized from the same Bosque program, manipulating just one database. On other phylogenetics programs you should be very careful creating folders and filenames ad-hoc to keep certain order when the phylogenetic analyses are complex.
* Networking Computing. While most phylogenetic programs uses only local computational resources (for instance they just run on the local computer) Bosque has been designed with the client-server concept in mind. This is particularly important in phylogenetics because some analyses may take a considerable amount of time to finish and if we are limited to run programs only on the local computer then we need to leave the computer turned on and almost dedicated to that job. In Bosque it is possible to use remote servers to execute actual programs. The Bosque Server will accept jobs from previously registered users over the network. If the server is busy then it will queue the job and will run it when the previous jobs on server finish. In this process a Bosque client can disconnect from the server and return to it just to ask if the job has finished. If it is finished then the user can download the output and continue the analyses.
System Requirements:No special requirements.
Program Release Status: New Release
Program Install Support: Install and Uninstall