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

ã Cédric Notredame, Centro de Regulacio Genomica, 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 and Feedback. 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 NCBI BLAST Client 15

Using another Client 15

Using a BLAST local version on UNIX.. 16

Using a BLAST local version on Windows/cygwin. 16

Installing Other Companion Packages. 17

Installation of PSI-Coffee and Expresso. 18

Installation of M-Coffee. 19

Automated Installation. 19

Manual Installation. 20

Installation of APDB and iRMSD.. 21

Installation of tRMSD.. 21

Installation of seq_reformat 22

Installation of extract_from_pdb. 22

Installation of 3D-Coffee/Expresso. 22

Automated Installation. 22

Manual Installation. 23

Installing Fugue for T-Coffee. 23

Installation of R-Coffee. 23

Automated Installation. 24

Manual Installation. 24

Installing ProbbonsRNA for R-Coffee. 24

Installing Consan for R-Coffee. 24

Quick Start 25

T-COFFEE.. 25

M-Coffee. 25

Expresso. 26

R-Coffee. 26

iRMSD and APDB.. 27

tRMSD.. 27

MOCCA.. 28

Recent Modifications. 29

Reference Manual 30

Environment Variables. 30

http_proxy_4_TCOFFEE.. 30

email_4_TCOFFEE.. 31

DIR_4_TCOFFEE.. 31

TMP_4_TCOFFEE.. 31

CACHE_4_TCOFFEE.. 31

NO_ERROR_REPORT_4_TCOFFEE.. 31

PDB_DIR.. 31

NO_WARNING_4_TCOFFEE.. 31

Setting up the T-Coffee environment variables. 31

Well Behaved Parameters. 32

Separation. 32

Posix. 32

Entering the right parameters. 32

Parameters Syntax. 32

No Flag. 32

-parameters. 33

-t_coffee_defaults. 33

-mode. 33

-score [Deprecated]. 34

-evaluate. 34

-convert [cw]. 34

-do_align [cw]. 34

Special Parameters. 35

-version. 35

-proxy. 35

-email 35

-check_configuration. 35

-cache. 35

-update. 35

-full_log. 35

-other_pg. 36

Input 36

Sequence Input 36

-infile [cw]. 36

-in (Cf –in from the Method and Library Input section) 36

-get_type. 36

-type [cw]. 36

-seq. 37

-seq_source. 37

Structure Input 37

-pdb. 37

Tree Input 37

-usetree. 37

Structures, Sequences Methods and Library Input via the in Flag. 38

-in. 38

Profile Input 40

-profile. 40

-profile1 [cw]. 40

-profile2 [cw]. 40

Alignment Computation. 40

Library Computation: Methods. 40

-lalign_n_top. 40

-align_pdb_param_file. 41

-align_pdb_hasch_mode. 41

Library Computation: Extension. 41

-lib_list [Unsupported]. 41

-do_normalise. 41

-extend. 41

-extend_mode. 41

-max_n_pair. 42

-seq_name_for_quadruplet 42

-compact 42

-clean. 42

-maximise. 42

-do_self 42

-seq_name_for_quadruplet 42

-weight 43

Tree Computation. 43

-distance_matrix_mode. 43

-quicktree [CW]. 44

Pair-wise Alignment Computation. 44

-dp_mode. 44

-ktuple. 45

-ndiag. 45

-diag_mode. 45

-diag_threshold. 46

-sim_matrix. 46

-matrix [CW]. 46

-nomatch. 46

-gapopen. 46

-gapext 47

-fgapopen. 47

-fgapext 47

-cosmetic_penalty. 47

-tg_mode. 47

Weighting Schemes. 47

-seq_weight 47

Multiple Alignment Computation. 48

-msa_mode. 48

-one2all 48

-profile_comparison. 48

-profile_mode. 49

Alignment Post-Processing. 49

-clean_aln. 49

-clean_threshold. 49

-clean_iteration. 49

-clean_evaluation_mode. 49

-iterate. 49

CPU Control 50

Multithreading. 50

-multi_thread [NOT Supported]. 50

Limits. 50

-mem_mode. 50

-ulimit 50

-maxlen. 50

Aligning more than 100 sequences with DPA.. 50

-maxnseq. 50

-dpa_master_aln. 50

-dpa_maxnseq. 51

-dpa_min_score1. 51

-dpa_min_score2. 51

-dap_tree [NOT IMPLEMENTED]. 51

Using Structures. 51

Generic. 51

-mode. 51

-check_pdb_status. 52

3D Coffee: Using SAP.. 52

Using/finding PDB templates for the Sequences. 52

-template_file. 52

-struc_to_use. 54

Multiple Local Alignments. 54

-domain/-mocca. 55

-start 55

-len. 55

-scale. 55

-domain_interactive [Examples]. 56

Output Control 57

Generic. 57

Conventions Regarding Filenames. 57

Identifying the Output files automatically. 57

-no_warning. 57

Alignments. 57

-outfile. 57

-output 57

-outseqweight 58

-case. 58

-cpu. 58

-outseqweight 58

-outorder [cw]. 59

-inorder [cw]. 59

-seqnos. 59

Libraries. 59

-out_lib