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03.27.2017

PIVOT released (replacing IDV); an extensive R-based GUI for the visualization and analysis of RNASeq data.

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11.09.2016

PESS has been released and is available for download with source code on GitHub.

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03.02.2016

VERSE RNASeq quantifier has been released and is available for download.

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10.21.2014

NoFold released with source code available via GitHub.

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CRIMSON

Maintained by Stephen Fisher License (pdf)

Subtree extraction from very large phylogenetic trees

Crimson facilitates the extraction of sub-trees from very large phylogenetic trees. Trees are loaded into a shared database and sampled according to schemes controlled by the user. Comprehensive graphical dialogs allow users to easily manage and query trees in the database. Queries can be stored in the database to be shared with other users and moved between databases. A command line interface enables users to write their own function and scripts to manager the database, manipulate the trees and queries, and automate any of the built-in functions.

This application has been tested on Windows and Linux systems and should run on any system that contains Java 1.5 or later. Both Oracle and MySQL databases can be used.

Crimson was created as part of the Cyberinfrastructure for Phylogenetic Research (CIPRES) project.

Screen shots...

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CIPRES Dataset

When Crimson was created, we included access to an Oracle database with a 1 million-taxon tree (see CIPRES Simulation Data), although Crimson can be used with any similarly formatted dataset. The online database is no longer accessible, so we're making available a dump of the Oracle database. The database requires 2 TB of space (4 TB when loading the data) and the data dump should work with Oracle 10 or 11. The database dump is available here.