Manual CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE Cédric Notredame T-Coffee User Guide and Reference Manual T-Coffee User Guide (Version 2.40, April 2005) Cédric Notredame and Centre National De La Recherche Scientifique T-COFFEE REFERENCE MANUAL License and Terms of Use ................................................................................... ................................ ......................... 666 T-Coffee is distributed under the Gnu Public License................................................................................................6 T-Coffee code can be re-used freely..............................................................................................................................6 Addresses and Contacts ................................................................................... ................................ ............................... 777 Contributors ...................................................................................................................................................................7 Addresses.........................................................................................................................................................................7 CitationsCitations.................................................................................................................................................................................................................. .................. 888 T-Coffee...........................................................................................................................................................................8 Mocca ..............................................................................................................................................................................9 CORE ............................................................................................................................................................................10 Other Contributions.....................................................................................................................................................10 What Is TT----COFFEECOFFEE ? ................................................................................... ....................................... 111111 What is T-Coffee?.........................................................................................................................................................11 What does it do? ......................................................................................................................................................11 What can it align?....................................................................................................................................................11 How can I use it?.....................................................................................................................................................11 Is T-Coffee different from ClustalW?.......................................................................................................................11 What T-Coffee Can and Cannot do for you …..........................................................................................................12 (NOT) Fetching Sequences......................................................................................................................................12 Aligning Sequences..................................................................................................................................................12 Combining Alignments ............................................................................................................................................12 Evaluating Alignments.............................................................................................................................................12 Combining Sequences and Structures......................................................................................................................12 Identifying Occurrences of a Motif: Mocca.............................................................................................................13 How Does T-Coffee works ...........................................................................................................................................13 InstallationInstallation............................................................................................................................................................................................................ ............ 141414 Standard Installation ...................................................................................................................................................14 Extended Installation and other Packages .................................................................................................................15 Quick StartStart............................................................................................................................................................................................................ ............ 161616 T-COFFEE....................................................................................................................................................................16 MOCCA ........................................................................................................................................................................16 Recent Modifications ................................................................................... ..................................... 171717 Manual ................................................................................... ............................................................................................... .................. 181818 Using T-Coffee..............................................................................................................................................................18 Standard Alignments................................................................................................................................................18 Alignment Combination...........................................................................................................................................18 Aligning Sequences and Structures.............................................................................................................................18 Aligning Sequences and Profiles .................................................................................................................................19 Using Structures (Or templates) Within Profiles.....................................................................................................19 Using New and Existing Methods ...............................................................................................................................19 Using Methods Integrated in T-Coffee ....................................................................................................................19 Integrating External Methods..................................................................................................................................21 Managing a collection of method files.....................................................................................................................22 Advanced Method Integration .................................................................................................................................22 The Mother of All method files….............................................................................................................................23 Creating Your Own T-Coffee Libraries.....................................................................................................................25 Using Pre-Computed Alignments ............................................................................................................................25 111 T-COFFEE REFERENCE MANUAL Customizing the Weighting Scheme.........................................................................................................................25 Generating Your Own Libraries..............................................................................................................................25 Frequently Asked Questions ................................................................................. ................................ ................. 262626 Abnormal Terminations and Wrong Results.............................................................................................................26 Q: The program keeps crashing when I give my sequences ....................................................................................26 Q: The default alignment is not good enough..........................................................................................................26 Q: The alignment contains obvious mistakes...........................................................................................................26 Q: The program is crashing ....................................................................................................................................26 Q: I am running out of memory ...............................................................................................................................27