TCW v2.8 (5Sept2018) -- 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.

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     Documentation   Summary          inputs, outputs and processing Index of documentation pages     Tour   runAS obtain UniProt and GO for input to runSingleTCW runSingleTCW build single species annotated database runDE add differential expression viewSingleTCW query results of a single species database runMultiTCW build multi-species comparison database viewMultiTCW query results of multi-species database     Demos   Java Applets     demos contained in package     Recent Features   ORF finder The algorithm uses hit information and on-the-fly training for a 5th-order Markov score. Fast searching Integration of diamond and usearch for fast annotation. Locations Location information (e.g. chromosome, start, end) can be entered. Differential Expression Users can supply a file of R commands for DE computation, or use built-in computations.     Reference   C. Soderlund, W. Nelson, M. Willer and D. Gang. (2013) TCW: Transcriptome Computational Workbench. PLoS ONE Link     NSF Disclaimer   Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Figure 1: viewSingleTCW - result of a query on DE values. Figure 2: Computed ORF using hit coordinates as a guide. Figure 3: viewMultiTCW - dynamic programming alignment of a BBH cluster.