April, 2005

T-COFFEE (version 2.xx)

§ Installation Notes

§ Technical Notes

§ Documentation

§ Tutorial

§ F.A.Q

Cedric Notredame (cedric.notredame@europe.com)

Table of Contents

T-COFFEE (version 2.00) 1

§ Installation Notes. 1

§ Technical Notes. 1

§ Documentation.. 1

§ Tutorial.. 1

§ F.A.Q.. 1

License and Terms of Use.. 9

Addresses and Contacts. 10

Citations. 11

T-Coffee.. 11

Mocca.. 12

DESCRIPTION.. 13

What is T-Coffee?. 13

What does it do?. 13

What can it align?. 13

How can I use it?. 13

Is T-Coffee different from ClustalW?. 13

What Can T-Coffee do for you (and what it cannot do) 14

(NOT) Fetching Sequences. 14

Aligning Sequences. 14

Combining Alignments. 14

Evaluating Alignments