TCW v1.6.4 (21-Sept-2016) -- see Release Notes. TCW provides analysis and query for sequences (transcriptome, proteome), and comparison of species sequences. TCW uses Java, mySQL, optionally R, and various External packages. It has been tested on Linux and Mac.

Documentation Summary - inputs, outputs and processing   Index - into documentation pages     Download TCW package - jars, demos, external packages, R scripts   TCW source - source code for developers   TCW update - jars and R-scripts only for TCW updates

Tour viewSingleTCW - query results of a single species database   runSingleTCW - build single species annotated database   runDE - add differential expression     viewMultiTCW - query comparison results   runMultiTCW - build comparison database Demos   Java Applets - demos contained in package

Recent Releases:

1. Fast searching in TCW: Integration of diamond and usearch for fast annotation.
2. Location information: Location information (e.g. chromosome, start, end) can be entered.
3. ORF finder: The algorithm uses hit information and on-the-fly training of usage along with Start/Stop codons.
4. Differential Expression: Users can supply a file of R commands for DE computation, or use built-in computations.
5. Release Notes: Provides information on other updates.

References

1. C. Soderlund, W. Nelson, M. Willer and D. Gang. (2013) TCW: Transcriptome Computational Workbench. PLoS ONE Link
2. C. Soderlund, E. Johnson, M. Bomhoff, and A. Descour. (2009) PAVE: Program for Assembling and Viewing ESTs. BMC Genomics 10:400. Link
3. C. Soderlund, W. Nelson and S. Goff (2014) Allele Workbench: transcriptome pipeline and interactive graphics for allele-specific expression. PLOS ONE. Link