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Technical

Centre National De LA Recherche scientifique (France)
CeNTRO De REGULACIO GENOMICA (SPAIN)
Cédric Notredame
www.tcoffee.org

T-Coffee:
Technical Documentation



T-Coffee Technical Documentation
(Version 8.01, July 2009)
www.tcoffee.org

T-Coffee, seq_reformat
PSI-Coffee, 3D-Coffee, M-Coffee, R-Coffee, APDB, iRMSD, T-RMSD

( Cédric Notredame, Centro de RegulacioGenomica, Centre National de la Recherche Scientifique, France
License and Terms of Use 6
T-Coffee is distributed under the Gnu Public License 6
T-Coffee code can be re-used freely 6
T-Coffee can be incorporated in most pipelines: Plug-in/Plug-out… 6

Addresses and Contacts 7
Contributors 7
Addresses 7

Citations 8
T-Coffee 8
Mocca 9
CORE 10
Other Contributions 10
Bug Reports andFeedback 10

Installation of The T-Coffee Packages 11
Third Party Packages and On Demand Installations 11
Standard Installation of T-Coffee 11
Unix 11
Microsoft Windows/Cygwin 13
MAC osX, Linux 13
CLUSTER Installation 13
If you have PDB installed: 13
Installing BLAST for T-Coffee 14
Why Do I need BLAST with T-Coffee? 14
Using the EBI BLAST Client 14
Using the NCBIBLAST Client 15
Using another Client 15
Using a BLAST local version on UNIX 16
Using a BLAST local version on Windows/cygwin 17
Installing Other Companion Packages 17
Installation of PSI-Coffee and Expresso 19
Installation of M-Coffee 19
Automated Installation 19
Manual Installation 20
Installation of APDB and iRMSD 22
Installation of tRMSD 22
Installation of seq_reformat22
Installation of extract_from_pdb 22
Installation of 3D-Coffee/Expresso 23
Automated Installation 23
Manual Installation 23
Installing Fugue for T-Coffee 24
Installation of R-Coffee 24
Automated Installation 24
Manual Installation 24
Installing ProbbonsRNA for R-Coffee 25
Installing Consan for R-Coffee 25

Quick Start 26
T-COFFEE 26
M-Coffee 26
Expresso 27R-Coffee 27
iRMSD and APDB 28
tRMSD 28
MOCCA 29

Recent Modifications 30

Reference Manual 31
Environment Variables 31
http_proxy_4_TCOFFEE 31
email_4_TCOFFEE 32
DIR_4_TCOFFEE 32
TMP_4_TCOFFEE 32
CACHE_4_TCOFFEE 32
PLUGINS_4_TCOFFEE 32
NO_ERROR_REPORT_4_TCOFFEE 32
PDB_DIR 32
NO_WARNING_4_TCOFFEE 32
UNIQUE_DIR_4_TCOFFEE 32
Setting up the T-Coffeeenvironment variables 32
Well Behaved Parameters 33
Separation 33
Posix 33
Entering the right parameters 33
Parameters Syntax 34
No Flag 34
-parameters 34
-t_coffee_defaults 35
-mode 35
-score [Deprecated] 35
-evaluate 35
-convert [cw] 36
-do_align [cw] 36
Special Parameters 36
-version 36
-proxy 36
-email 36
-check_configuration 36-cache 37
-update 37
-full_log 37
-plugins 37
-other_pg 37
Input 38
Sequence Input 38
-infile [cw] 38
-in (Cf –in from the Method and Library Input section) 38
-get_type 38
-type [cw] 38
-seq 38
-seq_source 38
Structure Input 39
-pdb 39
Tree Input 39
-usetree 39
Structures, Sequences Methods and Library Input via the ?in Flag 39
-in40
Profile Input 41
-profile 41
-profile1 [cw] 42
-profile2 [cw] 42
Alignment Computation 42
Library Computation: Methods 42
-lalign_n_top 42
-align_pdb_param_file 42
-align_pdb_hasch_mode 42
Library Computation: Extension 42
-lib_list [Unsupported] 42
-do_normalise 43
-extend 43
-extend_mode 43
-max_n_pair 43
-seq_name_for_quadruplet44
-compact 44
-clean 44
-maximise 44
-do_self 44
-seq_name_for_quadruplet 44
-weight 44
Tree Computation 45
-distance_matrix_mode 45
-quicktree [CW] 45
Pair-wise Alignment Computation 46
-dp_mode 46
-ktuple 47
-ndiag 47
-diag_mode 47
-diag_threshold 47
-sim_matrix 47
-matrix [CW] 48
-nomatch 48
-gapopen 48
-gapext 48...