1. Clustal W and Clustal X version 2.0 김영호, 박준호, 최현희 The 9 th Protein Folding Winter School

2. The Paper

3. Abstract  The Clustal W and Clustal X multiple sequence alignment programs have been completely rewritten in C++  This will facilitate the further development of the alignment algorithms in the future  This has allowed proper porting of the programs to the latest versions of Linux, Macintosh and Windows operating systems

4. Introduction1 Contents Clustal W 2.0 and Clustal X 2.02 New Features3 Related Sources4

5. Introduction  One of the oldest and most widely used  First distributed by post on floppy disks (late 1980s, witten in Microsoft Fortran for MS-DOS)  Clustal 1 ~ Clustal 4 (1988, 1989, IBM compatible PCs)  Clustal V (1992, VAX/VMS, Unix, Apple Macintosh, IBM compatible PCs)

6. Introduction  Clustal W and Clustal X (late 1990s)  Other powerful tools  BAliBASE  T-Coffee  MAFFT  MUSCLE  Yet, Clustal W and Clustal X continue to be very widely used. (EBI Clustal site gets millions of multiple alignment jobs per yr)

7. Introduction  Clustal W and Clustal X  W : Command terminal  X : Graphic  Procedure Sequence input (choose a chain or domain from each FASTA sequence) Concatenate all the query sequences in one file Run Output (score, alignment)

8. Clustal W 2.0 and Clustal X 2.0  What’s new?  Rewritten in C++  Easier to maintain the code  Easier to modify, replace some of the alignment algorithms.  UPGMA guide trees  Alternative to the NJ guide trees  Speeds up the alignment of large data sets  Iterative alignment facility  Increase alignment accuracy

9. Clustal W 2.0 and Clustal X 2.0  Clustal X Developed using NCBI’s vibrant toolbox The vibrant toolbox is no longer supported  Clustal X 2.0 Rewritten using the Qt GUI toolbox Qt GUI toolbox provides a native look and feel on Windows, Linux and Mac platforms`

10. New Features  UPGMA Faster than NJ (takes less than a minute to cluster 10,000 sequences while NJ takes over an hour) Slightly less accurate than BAliBASE benchmark, but on large alignments this is offset by the savings in processing time (2h vs. 12h)

11. New Features  Iteration A quick and effective method of refining alignments. ‘Remove first’ iteration scheme WSP (Weighted Sum of Pairs) During each iteration step, each sequence is removed form the alignment in turn and realigned. If the WSP score is reduced then the resulting alignment is retained.

12. New Features  Command line option ‘-clustering=UPGMA’ Calls algorithm for UPGMA ‘-iteration=alignment’ Refines the final alignment Less accurate but faster ‘-iteration=tree’ Refines at each step in the progressive alignment More accurate but slower ‘-numiters’ Sets iteration cycles (default: 3)

13. Related Sources  EBI Website European Bioinformatics Institute website Supports several alignment programs We can try various programs (Eg. ClustalW, MAFFT, T-coffee, MUSCLE etc.)

14. Related Sources  Clustal (web)

15. Related Sources  Clustal (dos)

16. Related Sources  Clustal (dos)

18. Related Sources  MUSCLE

19. Related Sources  T-Coffee

20. Related Sources  MAFFT

21. Related Sources  Kalign