t Coffee manual

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T-Coffee Technical Documentation

(Version 8.01, July 2009).tcoffee.or!

T-Coffee, se"#reformat

$%&-Coffee, 'D-Coffee, -Coffee, -

Coffee, *$D+, i%D, T-%D

Cdric Notredame* Ce'tro de Re#acio Ge'omica* Ce'tre Natio'a de a Rec&erc&eScie'ti+,e* Fra'ce


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icense an Terms of 0se...............................................3

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

*resses an Contacts..................................................4

Contributors.....................................................................................................................................................................

!ddresses..........................................................................................................................................................................

Citations.........................................................................8

T-Coffee............................................................................................................................................................................."

#occa................................................................................................................................................................................$

C%&'..............................................................................................................................................................................()

%ther Contributions......................................................................................................................................................()

*ug &eports and +eedbac,...........................................................................................................................................()

&nstallation of The T-Coffee $ac5a!es...........................11

Third Party Pac,ages and %n emand nstallations.................................................................................................((

tandard nstallation of T-Coffee........................................................................................................................... ......((

Unix...........................................................................................................................................................................11

Microsoft Windows/Cygwin................................................................................................................................... ...13

MAC osX, Linux........................................................................................................................................................13

CLUSTER nst!""!tion..............................................................................................................................................13

f you #!$% &'( inst!""%d)........................................................................................................................................13

nstalling *L!T for T-Coffee.....................................................................................................................................(0

W#y 'o n%%d (LAST wit# T*Coff%%+......................................................................................................................1

Using t#% E( (LAST C"i%nt.....................................................................................................................................1

Using t#% -C( (LAST C"i%nt..................................................................................................................................1

Using !not#%r C"i%nt................................................................................................................................................1Using ! (LAST "oc!" $%rsion on U-X....................................................................................................................1

Using ! (LAST "oc!" $%rsion on Windows/cygwin...................................................................................................10

nstalling %ther Companion Pac,ages........................................................................................................................(

nstallation of P-Coffee and '1presso......................................................................................................................($

nstallation of #-Coffee................................................................................................................................................($

Auto!t%d nst!""!tion............................................................................................................................. ......... .......12

M!nu!" nst!""!tion...................................................................................................................................... ......... ...4

nstallation of !P* and i.................................................................................................................................22

nstallation of t...................................................................................................................................................22

nstallation of se34reformat..........................................................................................................................................22

nstallation of e1tract4from4pdb..................................................................................................................................22

nstallation of 5-Coffee/'1presso...............................................................................................................................25

Auto!t%d nst!""!tion............................................................................................................................. ......... .......3M!nu!" nst!""!tion...................................................................................................................................... ......... ...3

nst!""ing 5ugu% for T*Coff%%....................................................................................................................... ......... ...

nstallation of &-Coffee.................................................................................................................................................20

Auto!t%d nst!""!tion............................................................................................................................. ......... .......

M!nu!" nst!""!tion...................................................................................................................................... ......... ...

nst!""ing &ro66onsR-A for R*Coff%%................................................................................................................. .....

nst!""ing Cons!n for R*Coff%%.................................................................................................................................

6uic5 %tart....................................................................23

T-C%++''......................................................................................................................................................................26

#-Coffee.........................................................................................................................................................................26

'1presso..........................................................................................................................................................................2

&-Coffee..........................................................................................................................................................................2

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i and !P*.........................................................................................................................................................2"

t............................................................................................................................................................................2"

#%CC!..........................................................................................................................................................................2$

)ecent (oifications.....................................................'

)eference (anual..........................................................'1

'nironment 7ariables................................................................................................................................................. .5(

#tt787roxy88TC955EE..........................................................................................................................................31

%!i"88TC955EE..................................................................................................................................................3

'R88TC955EE............................................................................................................................................... .....3

TM&88TC955EE...................................................................................................................................................3

CAC:E88TC955EE..............................................................................................................................................3

&LU;-S88TC955EE................................................................................................................................. .........3

-98ERR9R8RE&9RT88TC955EE......................................................................................................................3

&'(8'R..................................................................................................................................................................3

-98WAR--;88TC955EE..................................................................................................................................3

U-..................................................................................................................................................3

*%$!"u!t%...................................................................................................................................................................3

*con$%rt =cw>............................................................................................................................................................3*do8!"ign =cw>..........................................................................................................................................................3

pecial Parameters........................................................................................................................................................56

*$%rsion.....................................................................................................................................................................3

*7roxy........................................................................................................................................................................3

*%!i"........................................................................................................................................................................3

*c#%c?8configur!tion................................................................................................................................................3

*c!c#%........................................................................................................................................................................30

*u7d!t%......................................................................................................................................................................30

*fu""8"og....................................................................................................................................................................30

*7"ugins.....................................................................................................................................................................30

*ot#%r87g..................................................................................................................................................................30

nput................................................................................................................................................................................5"

S%@u%nc% n7ut..........................................................................................................................................................3*infi"% =cw>................................................................................................................................................................3

*in BCf in fro t#% M%t#od !nd Li6r!ry n7ut s%ctionD...........................................................................................3

*g%t8ty7%...................................................................................................................................................................3

*ty7% =cw>..................................................................................................................................................................3

*s%@............................................................................................................................................................................3

*s%@8sourc%...............................................................................................................................................................3

Structur% n7ut..........................................................................................................................................................32

*7d6...........................................................................................................................................................................32

Tr%% n7ut..................................................................................................................................................................32

*us%tr%%......................................................................................................................................................................32

Structur%s, S%@u%nc%s M%t#ods !nd Li6r!ry n7ut $i! t#% in 5"!g ......................................................................32

*in..............................................................................................................................................................................4

&rofi"% n7ut..............................................................................................................................................................1

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*7rofi"%......................................................................................................................................................................1

*7rofi"%1 =cw>............................................................................................................................................................

*7rofi"% =cw>............................................................................................................................................................

!lignment Computation................................................................................................................................................02

Li6r!ry Co7ut!tion) M%t#ods........................................................................................................................... .....

*"!"ign8n8to7............................................................................................................................................................

*!"ign87d687!r!8fi"%.............................................................................................................................................

*!"ign87d68#!sc#8od%...........................................................................................................................................

Li6r!ry Co7ut!tion) Ext%nsion......................................................................................................................... .....

*"i68"ist =Unsu77ort%d>.............................................................................................................................................

*do8nor!"is%...........................................................................................................................................................3

*%xt%nd......................................................................................................................................................................3

*%xt%nd8od%............................................................................................................................................................3

*!x8n87!ir..............................................................................................................................................................3

*s%@8n!%8for8@u!dru7"%t.......................................................................................................................................

*co7!ct...................................................................................................................................................................

*c"%!n........................................................................................................................................................................

*!xiis%..................................................................................................................................................................

*do8s%"f.....................................................................................................................................................................

*s%@8n!%8for8@u!dru7"%t.......................................................................................................................................

*w%ig#t......................................................................................................................................................................

Tr%% Co7ut!tion.....................................................................................................................................................

*dist!nc%8!trix8od%............................................................................................................................................

*@uic?tr%% =CW>........................................................................................................................................................

&!ir*wis% A"ign%nt Co7ut!tion............................................................................................................................

*d78od%..................................................................................................................................................................

*?tu7"%.......................................................................................................................................................................0

*ndi!g........................................................................................................................................................................0

*di!g8od%...............................................................................................................................................................0

*di!g8t#r%s#o"d.........................................................................................................................................................0

*si8!trix...............................................................................................................................................................0*!trix =CW>............................................................................................................................................................

*no!tc#...................................................................................................................................................................

*g!7o7%n...................................................................................................................................................................

*g!7%xt......................................................................................................................................................................

*fg!7o7%n..................................................................................................................................................................

*fg!7%xt.....................................................................................................................................................................

*cos%tic87%n!"ty.....................................................................................................................................................

*tg8od%...................................................................................................................................................................2

W%ig#ting Sc#%%s...................................................................................................................................................2

*s%@8w%ig#t...............................................................................................................................................................2

Mu"ti7"% A"ign%nt Co7ut!tion................................................................................................................... ......... .2

*s!8od%................................................................................................................................................................2

*on%!"".....................................................................................................................................................................2*7rofi"%8co7!rison..................................................................................................................................................4

*7rofi"%8od%............................................................................................................................................................4

A"ign%nt &ost*&roc%ssing.......................................................................................................................................4

*c"%!n8!"n.................................................................................................................................................................4

*c"%!n8t#r%s#o"d.......................................................................................................................................................1

*c"%!n8it%r!tion........................................................................................................................................................1

*c"%!n8%$!"u!tion8od%...........................................................................................................................................1

*it%r!t%......................................................................................................................................................................1

CP9 Control...................................................................................................................................................................(

Mu"tit#r%!ding....................................................................................................................................................... ...1

*u"ti8cor%................................................................................................................................................................1

*n8cor%......................................................................................................................................................................

Liits................................................................................................................................................................ ........

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*%8od%...............................................................................................................................................................

*u"iit........................................................................................................................................................................

*!x"%n.....................................................................................................................................................................

A"igning or% t#!n 144 s%@u%nc%s wit# '&A...........................................................................................................

*!xns%@...................................................................................................................................................................

*d7!8!st%r8!"n.......................................................................................................................................................3

*d7!8!xns%@...........................................................................................................................................................3

*d7!8in8scor%1......................................................................................................................................................3

*d7!8in8scor%......................................................................................................................................................3

*d!78tr%% =-9T M&LEME-TE'>..........................................................................................................................3

9sing tructures.............................................................................................................................................................0

;%n%ric.....................................................................................................................................................................

*od%........................................................................................................................................................................

*c#%c?87d68st!tus....................................................................................................................................................

3' Coff%%) Using SA&..............................................................................................................................................

Using/finding &'( t%7"!t%s for t#% S%@u%nc%s......................................................................................................

*t%7"!t%8fi"%............................................................................................................................................................

*struc8to8us%............................................................................................................................................................0

#ultiple Local !lignments............................................................................................................................................

*do!in/*occ!........................................................................................................................................................0

*st!rt..........................................................................................................................................................................0

*"%n............................................................................................................................................................................

*sc!"%.........................................................................................................................................................................

*do!in8int%r!cti$% =Ex!7"%s>..............................................................................................................................

%utput Control...............................................................................................................................................................$

;%n%ric.....................................................................................................................................................................2

Con$%ntions R%g!rding 5i"%n!%s...........................................................................................................................2

d%ntifying t#% 9ut7ut fi"%s !uto!tic!""y....................................................................................................... .........2

*no8w!rning..............................................................................................................................................................2

A"ign%nts........................................................................................................................................................ ........2

*outfi"%.......................................................................................................................................................................2*out7ut.......................................................................................................................................................................2

*outs%@w%ig#t............................................................................................................................................................4

*c!s%..........................................................................................................................................................................4

*c7u...........................................................................................................................................................................1

*outs%@w%ig#t............................................................................................................................................................1

*outord%r =cw>..........................................................................................................................................................1

*inord%r =cw>............................................................................................................................................................1

*s%@nos......................................................................................................................................................................1

Li6r!ri%s..................................................................................................................................................... .......... ....1

*out8"i6......................................................................................................................................................................

*"i68on"y....................................................................................................................................................................

Tr%%s..........................................................................................................................................................................

*n%wtr%%....................................................................................................................................................................&eliability 'stimation....................................................................................................................................................62

C9RE Co7ut!tion..................................................................................................................................................

*%$!"u!t%8od%.........................................................................................................................................................

Generic %utput..............................................................................................................................................................65

*run8n!%.................................................................................................................................................................3

*@ui%t.........................................................................................................................................................................3

*!"ign =CW>...............................................................................................................................................................3

!P*; i and t Parameters.....................................................................................................................65

*@ui%t =S!% !s T*Coff%%>.........................................................................................................................................

*run8n!% =S!% !s T*Coff%%>.................................................................................................................................

*!"n............................................................................................................................................................................

*n8%xc"ud%d8n6.........................................................................................................................................................

*!xiu8dist!nc%..................................................................................................................................................

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*sii"!rity8t#r%s#o"d.................................................................................................................................................

*"oc!"8od%..............................................................................................................................................................

*fi"t%r.........................................................................................................................................................................

*7rint8r!7d6 =Unsu77ort%d>.....................................................................................................................................

*outfi"% =S!% !s T*Coff%%>.......................................................................................................................................

*co"or8od%..............................................................................................................................................................

+uilin! a %erer...........................................................33

En$iron%nt !ri!6"%s..............................................................................................................................................

9ut7ut of t#% .dnd fi"%...............................................................................................................................................0

&%rissions...............................................................................................................................................................0

9t#%r &rogr!s........................................................................................................................................................0

ormats.........................................................................38

Parameter files...............................................................................................................................................................6"

e3uence

Technical /otes............................................................47

eelopment...................................................................................................................................................................0

Co!nd Lin% List...................................................................................................................................................0

To Do;..........................................................................43


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icense an Terms ofse

T-Coffee is istri:ute uner the =nu $u:lic

icense

Please make sure you have agreed with the terms of the license attached to thepackage before using the T-Coffee package or its documentation. T-Coffee is a

freeware open source distributed under a GPL license. This means that there arevery little restrictions to its use, either in an academic or a non academicenvironment.

T-Coffee coe can :e re-use freely

ur philosophy is that code is meant to be re-used, including ours. !o permission isneeded for the cut and paste of a few functions, although we are always happy toreceive pieces of improved code.

T-Coffee can :e incor>orate in most >i>elines?

$lu!-in@$lu!-out;

ur philosophy is to insure that as many methods as possible can be used as plug-ins within T-Coffee. Likewise, we will give as much support as possible to anyonewishing to turn T-Coffee into a plug-in for another method. "or more details on howto do this, see the plug-in and the plug-out sections of the Tutorial #anual.

$gain, you do not need our permission to either use T-Coffee %or your method as aplug-in&out' but if you let us know, we will insure the stability of T-Coffee withinyour system through future releases.

The current license only allows for the incorporation of T-Coffee in non-commercial

pipelines %i.e. where you do not sell the pipeline, or access to it'. (f your pipeline iscommercial, please get in touch with us.

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*resses anContacts

Contri:utors

T$co"ee i- de.eo/ed* mai'tai'ed* mo'itored* -ed a'd de0##ed 01 adedicated team t&at i'cde or &a.e i'cded%

Cdric Notredame* Fa0rice Armo#om* De- Hi##i'-* Se0a-tie'Moretti* Ora O2Si.a'! Eamo' O2Tooe* Oi.ier Poirot* 3ar-te'S&re* Iai' 4aace* A'drea- 4im

*resses

)e are always very eager to get some user feedback. Please do not hesitate to dropus a line at* cedric.notredame+europe.com The latest updates of T-Coffee arealways available on* www.tcoffee.org . n this address you will also find a link tosome of the online T-Coffee servers, including Tcoffee+igs

T-Coffee can be used to automatically check if an updated version is available,however the program will not update automatically, as this can cause endlessreproducibility problems.

PROMPT: t_coffee update

8
mailto:[email protected]:[email protected]


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Citations

(t is important that you cite T-Coffee when you use it. Citing us is %almost' likegiving us money* it helps us convincing our institutions that what we do is useful

and that they should keep paying our salaries and deliver onuts to our offices fromtime to time %!ot that they ever did it, but it would be nice anyway'.

Cite the server if you used it, otherwise, cite the original paper from %!o, itwas never named /T-Coffee /'.

!otredame C, 0iggins G,0eringa 1.

2elated $rticles, Links

T-Coffee* $ novel method for fast and accurate multiple se3uencealignment.

1 #ol 4iol. 5ep 678%9'*:-9;.P#(* 9:; ?Pub#ed - inde@ed for #AL(!AB

ther useful publications include*

T-Coffee

Claude 14, 5uhre ,!otredame C, Claverie 1#,$bergel C.


Casp2* a web server for automated molecular replacement usinghomology modelling.

!ucleic $cids 2es. > 1ul 978%)eb 5erver issue'*)==-= ?Pub#ed - inde@ed for #AL(!AB

Poirot , 5uhre , $bergel C,DToole A, !otredame C.


8Coffee+igs* a web server for combining se3uences andstructures into a multiple se3uence alignment.

!ucleic $cids 2es. > 1ul 978%)eb 5erver issue'*)8;->.P#(* 9:9:8>: ?Pub#ed - inde@ed for #AL(!AB

9
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10964570http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10964570http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=10964570http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15215460http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15215460http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15215460http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=15215460http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15215345http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15215345http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=15215345http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10964570http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10964570http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=10964570http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15215460http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15215460http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15215460http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=15215460http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15215345http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15215345http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=15215345


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D5ullivan , 5uhre ,$bergel C, 0iggins G,

!otredame C.


8Coffee* combining protein se3uences and structures withinmultiple se3uence alignments.

1 #ol 4iol. > 1ul 78>%'*86:-.P#(* 99898< ?Pub#ed - inde@ed for #AL(!AB

!otredame C, 0iggins G,0eringa 1.


T-Coffee* $ novel method for fast and accurate multiple se3uencealignment.1 #ol 4iol. 5ep 678%9'*:-9;.P#(* 9:; ?Pub#ed - inde@ed for #AL(!AB

!otredame C, 0olm L,0iggins G.


C""AA* an obEective function for multiple se3uence alignments.4ioinformatics. 9.P#(* 99898< ?Pub#ed - inde@ed for #AL(!AB

Chttp*&&www.tcoffee.org&Publications&Pdf&core.pp.pdf

1
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15201059http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15201059http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15201059http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=15201059http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12824354http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12824354http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=12824354http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11301309http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=11301309http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10964570http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10964570http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=10964570http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9682054http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9682054http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=9682054http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11301309http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=11301309&tool=ExternalSearchhttp://www.tcoffee.org/Publications/Pdf/core.pp.pdfhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15201059http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15201059http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15201059http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=15201059http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12824354http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12824354http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=12824354http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11301309http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=11301309http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10964570http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10964570http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=10964570http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9682054http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9682054http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=9682054http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11301309http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Display&dopt=pubmed_pubmed&from_uid=11301309&tool=ExternalSearchhttp://www.tcoffee.org/Publications/Pdf/core.pp.pdf


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ther Contri:utions

)e do not mean to steal code, but we will always try to re-use pre-e@isting codewhenever that code e@ists, free of copyright, Eust like we e@pect people to do withour code. 0owever, whenever this happens, we make a point at properly citing the

source of the original contribution. (f ever you recogniFe a piece of your codeimproperly cited, please drop us a note and we will be happy to correct that.

(n the mean time, here are some important pieces of code from other packages thathave been incorporated within the T-Coffee package. These include*

-The 5im algorithm of 0uang and #iller that given two se3uences computesthe ! best scoring local alignments.

-The tree reading&computing routines are taken from the Clustal) Package,courtesy of 1ulie Thompson, es 0iggins and Toby Gibson %Thompson, 0iggins,Gibson, 9=;8->=6,vol. , !ucleic $cid 2esearch'.

-The implementation of the algorithm for aligning two se3uences in linear

space was adapted from #yers and #iller, in C$4(5, 9


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&nstallation of The T-Coffee $ac5a!es

Thir $arty $ac5a!es an n Deman

&nstallations

T-Coffee is a comple@ package that interacts with many other third part software. (fyou only want a standalone version of T-Coffee, you may install that package on itsown. (f you want to use a most sophisticated flavor %8dcoffee, e@presso, rcofeee,etc...', the installer will try to install all the third party packages re3uired.

!ote that since version ;.:=, T-Coffee will use Don demandD installation and install

the third party packages it needs JwhenJ it needs them. This only works forpackages not re3uiring specific licenses and that can be installed by the regularinstaller. Please let us know if you would like another third party package to beincluded.

)henver on-demand installation or automated installation fails because ofunforessen system specificities, users should install the third party packagemanually. This documentation gives some tips we have found useful, but users areencouraged to check the original documentation.

%tanar &nstallation of T-Coffee

niA

Kou need to have* gcc, g;;, CP$! and an internet connection and your rootpassword %to install 5$P'. (f you cannot log as root, ask %kindly' your systemmanager to install 5$P**Lite for you. Kou may do this before or after theinstallation of T-Coffee. Aven without 5$P you will still be able to use the basicfunctions of T-Coffee %simplest usage'.

1. gunzip t_coffee.tar.gz2. tar -xvf t_coffee.tar3. cd t_coffee4. ./install t_coffee

This installation will only install the stand alone T-Coffee. (f you want to install a

12
http://search.cpan.org/~byrne/SOAP-Lite-0.60a/http://search.cpan.org/~byrne/SOAP-Lite-0.60a/


16/80

specific mode of T-Coffee, you may try the following commands that will try togather all the necessary third party packages. !ote that a package already found onyour system will not be re-installed.

./install t_coffee

./install mcoffee

./install 3dcoffee

./install rcoffee

./install psicoffee

r even

./install all

-$ll the corresponding e@ecutables will be downloaded automatically and installedin

$HOME/.t_coffee/plugins

-if you e@ecutables are in a different location, give it to T-Coffee using the -pluginsflag.

-(f the installation of any of the companion package fails, you should install ityourself using the provided link %see below' and following the authors instructions.

-(f you have not managed to install 5$P**Lite, you can re-install it later %from

anywhere' following steps 9-.

-This procedure attempts 8 things* installing and Compiling T-Coffee %C program',(nstalling and compiling T#align %"ortran', (nstalling and compiling5$P**Lite%Perl #odule'.

-(f you have never installed 5$P**Lite, CP$! will ask you many 3uestions* sayKes to all

-(f everything went well, the procedure has created in the bin directory twoe@ecutables* tIcoffee and T#align %#a,e sure these e1ecutables are on your

>P!T=?'

1'
http://zhang.bioinformatics.ku.edu/TM-align/http://search.cpan.org/~byrne/SOAP-Lite-0.60a/http://zhang.bioinformatics.ku.edu/TM-align/http://search.cpan.org/~byrne/SOAP-Lite-0.60a/


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icrosoft Binos@Cy!in

(nstall Cygwin

ownload The (nstaller %!T Cygwin&'

Click on view to list $LL the packages

5elect* gcc-core, make, wget

ptional* ssh, @emacs, nano

2un mkpasswd in Cywin %as re3uested when you start cygwin'

(nstall T-Coffee within Cygwin using the Hni@ procedure

*C os, inuA

#ake sure you have the eveloperDs kit installed %compilers and makefile'

"ollow the Hni@ Procedure

C%T &nstallation

(n order to run, T-Coffee must have a value for the httpIpro@y and for the A-mail. (norder to do so you can either*

e@port the following values*

e@port httpIpro@yI>ITC""AAM/pro@y/ or // if no pro@y

e@port A#$(LI>ITC""AAM/your email/

2

modify the file N&.tIcoffee&tIcoffeeIenv

2

add to your command line* tIcoffee O. -pro@yMpro@yQ -emailMemail

if you have no pro@y* tIcoffee O -pro@y -emailMemailQ

&f you hae $D+ installe?

$ssuming you have a standard P4 installation in your file system

seten !or e"port# P%_&R 'a(s

pat)*/data/structures/all/pd(/ORseten !or e"port# P%_&R 'a(s

pat)*/structures/diided/pd(/

(f you do not have P4 installed, donDt worry, tIcoffee will go and fetch anystructure it needs directly from the P4 repository. (t will simply be a bit slowerthan if you had P4 locally.

17
http://www.cygwin.com/http://www.cygwin.com/


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&nstallin! +*%T for T-Coffee

4L$5T is a program that search se3uence databases for homologues of a 3ueryse3uence. (t works for proteins and !ucleic $cids. (n theory 4L$5T is Eust a

package like any, but in practice things are a bit more comple@. To run well, 4L5T

re3uires up to date databases %that can be fairly large, like !2 or H!(P2T' and apowerful computer.

"ortunately, an increasing number of institutes or companies are now providing4L$5T clients that run over the net. (t means that all you need is a small programthat send your 3uery to the big server and gets the results back. This prevents youfrom the hassle of installing and maintaining 4L$5T, but of course it is less privateand you rely on the network and the current load of these busy servers.

Thanks to its interaction with 4L$5T, T-Coffee can gather structures and proteinprofiles and deliver an alignment significantly more accurate than the default youwould get with T-Coffee or any similar method.

Let us go through the various modes available for T-Coffee

Bhy Do & nee +*%T ith T-Coffee

The most accurate modes of T-Coffe scan the databases for templates that they useto align the se3uences. There are currently two types of templates for proteins*

structures %P4' that can be found by a blastp against the P4 database andprofiles that can be constructed with eiether a blastp or a psiblast against nr oruniprot.

These templates are automatically built if you use*

t_coffee '+ourse,* -mode e"presso

that fetches aand uses pdb templates, or

t_coffee '+our se,* -mode psicoffee

that fetches and uses profile templates, or

t_coffee '+our se,* -mode accurate

that does everything and tries to use the best template. !ow that you see whyit is useful letDs see how to get 4L$5T up and running, from the easy solution totailor made ones.

sin! the +& +*%T Client

This is by far the easiest %and the default mode'. The perl clients are already

incorporated in T-Coffeem and all you need is the 5$P**Lite perl library. (n theory,T-Coffee should have already installed this library during the standard installation.

1


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Ket, this re3uires having toot access. (f you did not have it at the time of theinstallation, or if you need your system administrator to install 5$P**Lite, simplyfollow the instruction provided on the website*

)ttp://searc).cpan.org/(+rne/O0P-1ite-2.2a

(t really is worth the effort, since the A4( is providing one of the best webserviceavailable around, and most notably, the only public psiblast via a web service.

$nother important point is that the A4( re3uires your A-mail address to process your3ueries. !ormally, T-Coffee should have asked you to provide this address. (f youhave not, or if you have provided a phony address, you should correct this bydirectly editing the file

/.t_coffee/email.t"t

*e Careful? (f you provide a fake A-mail, the A4( may suspend the service for allmachines associated with your (P address %that could mean your entire lab, or entireinstitute, or even the entire country or, but ( doubt it, the whole universe'.

sin! the /C+& +*%T Client

The !C4( is the ne@t best alternative. (n my hand it was always a bit slower andmost of all, it does not incorporate P5(-4L$5T %as a web sevice'. $ big miss. The

!C4( web blast client is a small e@ecutable that you should install on your systemfollowing the instructions given on this link

ftp://ftp.nc(i.ni).go/(last/e"ecuta(les/10TET

5imply go for netbl;download the e@ecutable that corresponds to your architecture%cygwin users should go for the win e@ecutable'. espite all the files that comealong the e@ecutable blastcl8 is a stand alone e@ecutable that you can safely move toyour R4(!.

$ll you will then need to do is to make sure that T-Coffee uses the right client, whenyou run it.

-(last_serer456%&

!o need for any A-mail here, but you donDt get psiblast, and whenever T-Coffeewants to use it, blastp will be used instead.

sin! another Client

Kou may have your own client %lucky you'. (f that is so, all you need is to make sure

that this client is complient with the blast command line. (f your client is namedfoo.pl, all you need to to is run T-Coffee with

13


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-(last_serer461&E5T_foo.pl

"oo will be called as if it were blastpgp, and it is your responsability to make sure it

can handle the following command line*

foo.pl -p 'met)od* -d 'd(* -i 'infile* -o 'outfile* -m 7

method can either be blastp or psiblast.

infile is a "$5T$ file

-m; triggers the #L output. T-Coffee is able to parse both the A4( #L outputand the !C4( #L output.

(f foo.pl behaves differently, the easiest will probably be to write a wrapper aroundit so that wrappedIfoo.pl behaves like blastpgp

sin! a +*%T local ersion on /&

(f you have blastpgp installed, you can run it instead of the remote clients by using*

-(last_serer41O601

The documnentation for blastpgp can be found on*

888.nc(i.nlm.ni).go/staff/tao/9R10P&/(lastpgp.)tml

and the package is part of the standard 4L$5T distribution

ftp://ftp.nc(i.ni).go/(last/e"ecuta(les/10TET

epending on your system, your own skills, your re3uirements and on moreparameters than ( have fingers to count, installing a 4L$5T server suited for yourneeds can range from a 9 minutes Eob to an achivement spread over severalgenerations. 5o at this point, you should roam the !C4( website for suitableinformation.

(f you want to have your own 4L$5T server to run your own databases, you shouldknow that it is possible to control both the database and the program used by4L$5T*

-protein_db: will specify the database used by all the psi-blast

modes-pdb_db: will specify the database used by the pdb modes

14


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sin! a +*%T local ersion on Binos@cy!in

"or those of you using cygwin, be careful. )hile cygwin behaves like a H!(system, the 4L$5T e@ecutable re3uired for cygwin %win8' is e@pecting)(!)5 path and not H!( path. This has three important conse3uences*

9- the ncbi file declaring the ata directory must be*

C*)(!)5&&ncbi.init ?at the root of your )(!)5B

- the address mentionned with this file must be )(!)5 formated, for instance,on my system*

ataMC*ScygwinShomeSnotredameSblastSdata

8- )hen you pass database addresses to 4L$5T, these must be in )indows format*

-proteinIdbM/c*&somewhere&somewhereelse&database/

%using the slash %&' or the andtislash %S' does not matter on new systems but ( wouldreommand against incorporating white spaces.

&nstallin! ther Com>anion $ac5a!es

T-Coffee is meant to interact with as many packages as possible, either for aligningor using predictions. (f you type

t_coffee

Kou will receive a list of supported packages that looks like the ne@t table. (n theory,most of these packages can be installed by T-Coffee

****** Pairwise e!uence "lignment #ethods:--------------------------------------------fast_pair built_inexon$_pair built_inexon%_pair built_inexon_pair built_inslow_pair built_inproba_pair built_inlalign_id_pair built_inse!_pair built_inexternprofile_pair built_inhh_pair built_inprofile_pair built_incdna_fast_pair built_incdna_cfast_pair built_inclustalw_pair ftp://www.ebi.ac.u&/pub/clustalwmafft_pair http://www.biophys.&yoto-u.ac.'p/(&atoh/programs/align/mafft/mafft'tt_pair http://www.biophys.&yoto-u.ac.'p/(&atoh/programs/align/mafft/mafftgins_pair http://www.biophys.&yoto-u.ac.'p/(&atoh/programs/align/mafft/dialigntx_pair http://dialign-tx.gobics.de/dialignt_pair http://dialign-t.gobics.de/

poa_pair http://www.bioinformatics.ucla.edu/poa/probcons_pair http://probcons.stanford.edu/

18


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muscle_pair http://www.drive).com/muscle/t_coffee_pair http://www.tcoffee.orgpcma_pair ftp://iole.swmed.edu/pub/P#"/&align_pair http://msa.cgb.&i.seamap_pair http://bio.math.ber&eley.edu/amap/proda_pair http://bio.math.ber&eley.edu/proda/

pran&_pair http://www.ebi.ac.u&/goldman-srv/pran&/consan_pair http://selab.'anelia.org/software/consan/

****** Pairwise tructural "lignment #ethods:--------------------------------------------align_pdbpair built_inlalign_pdbpair built_inextern_pdbpair built_inthread_pair built_infugue_pair http://www-cryst.bioc.cam.ac.u&/fugue/download.htmlpdb_pair built_insap_pair http://www-

cryst.bioc.cam.ac.u&/fugue/download.htmlmustang_pair http://www.cs.mu.oz.au/(arun/mustang/tmalign_pair http://zhang.bioinformatics.&u.edu/+#-align/

****** #ultiple e!uence "lignment #ethods:--------------------------------------------clustalw_msa ftp://www.ebi.ac.u&/pub/clustalwmafft_msa http://www.biophys.&yoto-u.ac.'p/(&atoh/programs/align/mafft/mafft'tt_msa http://www.biophys.&yoto-u.ac.'p/(&atoh/programs/align/mafft/mafftgins_msa http://www.biophys.&yoto-u.ac.'p/(&atoh/programs/align/mafft/

dialigntx_msa http://dialign-tx.gobics.de/dialignt_msa http://dialign-t.gobics.de/poa_msa http://www.bioinformatics.ucla.edu/poa/probcons_msa http://probcons.stanford.edu/muscle_msa http://www.drive).com/muscle/t_coffee_msa http://www.tcoffee.orgpcma_msa ftp://iole.swmed.edu/pub/P#"/&align_msa http://msa.cgb.&i.seamap_msa http://bio.math.ber&eley.edu/amap/proda_msa http://bio.math.ber&eley.edu/proda/pran&_msa http://www.ebi.ac.u&/goldman-srv/pran&/

,,,,,,, Prediction #ethods available to generate +emplates

-------------------------------------------------------------"plfold http://www.tbi.univie.ac.at/(ivo/"/##top www.enzim.hu/hmmtop/012 http://mig.'ouy.inra.fr/logiciels/gor34/wublast_clienthttp://www.ebi.ac.u&/+ools/webservices/services/wublastblastpgp_clienthttp://www.ebi.ac.u&/+ools/webservices/services/blastpgp5555555555555555555555555555555555555555555555555555555555

19


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&nstallation of $%&-Coffee an A>resso

P5(-Coffee is a mode of T-Coffee that runs a a Psi-4L$5T on each of yourse3uences and makes a multiple profile alignment. (f you do not have any structuralinformation, it is by far the most accurate mode of T-Coffee. To use it, you must

have 5$P installed so that the A4( 4L$5T client can run on your system.(t is a bit slow, but really worth it if your se3uences are hard to align and if theaccuracy of your alignment is important.

To use this mode, try*

t_coffee '+ourse,uence* -mode psicoffee

!ote that because P5(-4L$5T is time consuming, T-Coffee stores the runs in itscache %.&tcoffee&cache' so that it does not need to be re-run. (t means that if you re-

align your se3uences %or add a few e@tra se3uences', things will be considerablyfaster.

(f your installation procedure has managed to compile T#align, and if T-Coffee hasaccess to the A4( 4L$5T server %or any other server' you can also do the following*

t_coffee '+ourse,uence* -mode e"presso

That will look for structural templates. $nd if both these modes are running fine,then you are ready for the best, the /crme de la crme/*

t_coffee '+ourse,uence* -mode accurate

&nstallation of -Coffee

#-Coffee is a special mode of T-Coffee that makes it possible to combine the outputof many multiple se3uence alignment packages.

*utomate &nstallation

(n the T-Coffee distribution, type*

./install mcoffee

(n theory, this command should download and install every re3uired package. (f,however, it fails, you should switch to the manual installation %see ne@t'.

4y default these packages will be in

$HOME/.t_coffee/plugins

2


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(f you want to have these companion packages in a different directory, you caneither set the environement variable

P19&5_;_T6O


25/80

(f for some reason, you do not want this directory to be on your path, or you want tospecify a precise directory containing the e@ecutables, you can use*

e"port P19&5_;_T6O


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dna_diag_pro(_AB2_e"p_AA2222 dna_matri".scr

(f you would rather have the mcoffee directory in some other location, set the#C""AAI>ITC""AA environement variable to the propoer directory*

seten M6O


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&nstallation of eAtract#from#>:

E9tract68rom6/d0 i- a PD5 re8ormatti'# /ac7a#e t&at i- /art o8t6co"ee! To -e it (a'd -ee t&e a.aia0e o/tio'-)* t1/e!

t_coffee ot)er_pg apd( )

E9tract68rom6/d0 re,ire- #et i' order to atomatica1 8etc& PD5-trctre-!

&nstallation of 'D-Coffee@A>resso

8-Coffee&A@presso is a special mode of T-Coffee that makes it possible to combine

se3uences and structures. The main difference between A@presso and 8-Coffee isthat A@presso fetches the structures itself.



./install e"presso

OR

./install 3dcoffee

(n theory, this command should download and install every re3uired package%e1cept fugue'. (f, however, it fails, you should switch to the manual installation%see ne@t'.

anual &nstallation

(n order to make the most out of T-Coffee, you will need to install the followingpackages %make sure the e@ecutable is named as indicated below'*

Pac&age 7unction555555555555555555555555555555555555555555555555555---------------------------------------------------wget $8offee

"utomatic 8ownloading of tructures---------------------------------------------------sap structure/structure comparisonsobtain it from 6. +aylor; 3#-#


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---------------------------------------------------=last www.ncbi.nih.nlm.gov---------------------------------------------------7ugue* protein to structure alignment program

http://www-cryst.bioc.cam.ac.u&/fugue/download.html***1+ 1#P>?1@***

nce the package is installed, make sure make sure that the e@ecutable is on yourpath, so that tIcoffee can find it automatically.

The wublast client makes it possible to run 4L$5T at the A4( without having toinstall any database locally. (t is an ideal solution if you are only using e@pressooccasionally.

&nstallin! u!ue for T-CoffeeHses a standard fugue installation. Kou only need to install the following packages*

Eoy, melody, fugueali, sstruc, hbond

(f you have root privileges, you can install the common data in*

cp fugue&classdef.dat &data&fugue&5H45T&classdef.dat

otherwise

5etenv #ALKICL$55A"MlocationQ

5etenv #ALKI5H45TMfugue&allmat.dat

$ll the other configuration files must be in the right location.

&nstallation of -Coffee

2-Coffee is a special mode able to align 2!$ se3uences while taking into accounttheir secondary structure.



./install rcoffee

(n theory, this command should download and install every re3uired package%e@cept consan'. (f, however, it fails, you should switch to the manual installation%see ne@t'.

anual &nstallation

2-Coffee only re3uires the package ienna to be installed, in order to compute

multiple se3uence alignments. To make the best out of it, you should also have allthe packages re3uired by #-Coffee

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Pac&age 7unction555555555555555555555555555555555555555555555555555---------------------------------------------------consan -offee

omputes highly accurate pairwise "lignments***1+ 1#P>?1@***selab.'anelia.org/software/consan/

---------------------------------------------------"plfold omputes " secondary tructures

www.tbi.univie.ac.at/(ivo/"/---------------------------------------------------probcons" probcons.stanford.edu/---------------------------------------------------#-offee +-offee and the most common #" Pac&ages

cf #-offee in this installation guide.8 and upward* -in has will be deprecated and replaced by the flags* -profile,-method,-aln,-se3,-pdb

->.* -modeMdna is still available but not any more needed or supported. HsetypeMprotein or dna if you need to force things

-8.6* corrected a bug that prevents short se3uences from being correctly aligned

-Hse of + as a separator when specifying methods parameters

-The most notable modifications have to do with the structure of the input. "romversion ., all files must be tagged to indicate their nature %$* alignment, 5*5e3uence, L* LibraryO'. )e are becoming stricter, but thatWs for your own goodO

$nother important modification has to do with the flag -matri@* it now controls thematri@ being used for the computation

'1


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eference anual

This reference manual gives a list of all the flags that can be used to modify thebehavior of T-Coffee. "or your convenience, we have grouped them according totheir nature. To display a list of all the flags used in the version of T-Coffee you areusing %along with their default value', type*

PROMPT: t_coffee

r

PROMPT: t_coffee )elp

r

PROMPT: t_coffee )elp in

r any other parameter

nironment Varia:les

It i- /o--i0e to modi81 T$Co"ee2- 0e&a.ior 01 -etti'# a'1 o8 t&e8ooi'# e'.iro'eme't .aria0e-! O' t&e 0a-& -&e* -e e9/ort:AR;


36/80

gets superseded by the command line values %-pro@y and -email'

(f you have no pro@y, Eust set this value to an empty string.

email#7#TC

5et the A-mail values provided to web services called upon by T-Coffee. Can beover-riden by the flag *%!i".

D#TC

4y default this variable is set to R0#A&.tIcoffee. This is where T-Coffee e@pectsto find its cache, tmp dir and possibly any temporary data stored by the program.

T$#7#TC

4y default this variable is set to R0#A&.tIcoffee&tmp. This is where T-Coffeestores temporary files.

C*CE#7#TC4y default this variable is set to R0#A&.tIcoffee&cache. This is where T-Coffeestores any data e@pensive to obtain* pdb files, sap alignments....

$=&/%#7#TC

4y default all the companion packages are searched in the directory(2I>ITC""AA&plugins&5Q. This variable overrides the default. This variablecan also be overriden by the *7"uginsT-Coffee flag

/##$T#7#TC

4y default this variable is no set. 5et it if you do not want the program to generate averbose error output file %useful for running a server'.

$D+#D&

(ndicate the location of your local P4 installation.

/#B*/&/=#7#TC

5uppresses all the warnings.

/&6#D#TC

5ets*

(2I>ITC""AA

C$C0AI>ITC""AA

T#PI>ITC""AA

PLHG(!5I>ITC""AA

To the same uni3ue value. The string #H5T be a valid directory

''


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%ettin! u> the T-Coffee enironment aria:les

T$Co"ee ca' &a.e it- o' e'.iro'me't +e! T&i- e'.iro'me't i- 7e/ti' a +e 'amed =HOME>!t6co"ee>t6co"ee6e'. a'd ca' 0e edited! T&e.ae o8 a'1 e#a .aria0e ca' 0e modi+ed t&ro#& t&at +e! For

i'-ta'ce* &ere i- a' e9am/e o8 a co'+#ratio' +e &e' 'ot re,iri'#a /ro91!

http_proxy_2_+177DD5D#"3?_2_+177DD5cedric.notredameJeurope.com

IMPORTANT:

-pro"#' -email t_co/ee_en& en&

Bell +ehae $arameters

%e>aration

Kou can use any kind of separator you want %i.e. ,7 spaceQM'. The synta@ used inthis document is meant to be consistent with that of Clustal). 0owever, in order to

take advantage of the automatic filename compleation provided by many shells, youcan replace XMY and X,Y with a space.

$osiA

T-Coffee is not P5( compliant.

nterin! the ri!ht >arameters

There are many ways to enter parameters in T-Coffee, see the -parameter flag in

Parameters Priorityn general you @ill not need to use these complicated parameters. Aet; if you find

yourself typing long command lines on a regular basis; it may be @orth reading

this section.

%ne may easily feel confused @ith the arious manners in @hich the parameters

can be passed to t4coffee. The reason for these many mechanisms is that they

allo@ seeral leels of interention. +or instance; you may install t4coffee for all

the users and decide that the defaults @e proide are not the proper ones n

this case; you @ill need to ma,e your o@n t4coffee4default file.

'7


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Later on; a user may find that he/she needs to ,eep re-using a specific set of

parameters; different from those in t4coffee4default; hence the possibility to

@rite an e1tra parameter file: parameters. n summary:

-parameters B prompt parameters B -t4coffee4defaults B -mode

This means that -parameterssupersede all the others; @hile parameters proided

ia -special modeare the @ea,est.

$arameters %yntaA

No Flag

(f no flag is used Fyour s%@u%nc%G must be the first argument. 5ee format for furtherinformation.

PROMPT: t_coffee sample_se,A.fasta

)hich is e3uivalent to

PROMPT: t_coffee sample_se,A.fasta

)hen you do so, sample4se3(is used as a name prefi@ for every file the program outputs.

-parameters

9sage: -parametersparameters4fileefault: no parameters file

(ndicates a file containing e@tra parameters. Parameters read this way behave as if they hadbeen added on the right end of the command line that they either supersede%one valueparameter' or complete %list of values'. "or instance, the following file %parameter.file' couldbe used

*******sample_param_file.param********-in5sample_se!C.fasta;#fast_pair-output5msf_aln

**************************************


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PROMPT: t_coffee -parameters4sample_param_file.param

)ill cause tIcoffee to apply the fastIpair method onto to the se3uences contained in

sampleIse3.fasta. (f you wish, you can also pipe these arguments into tIcoffee, by namingthe parameter file /stdin/ %as a rule, any file named stdin is e@pected to receive its contentvia the stdin'

cat sample_param_file.param I t_coffee -parameters4stdin

-t_coffee_defaults

9sage: -t4coffee4defaultsfile4nameBefault: not used.

This flag tells the program to use some default parameter file for tIcoffee. The format of that

file is the same as the one used with -parameters. The file used is either*

9. file nameQ if a name has been specified

. H/.t4coffee4defaults if no file was specified

8. The file indicated by the environment variable TC%++''4'+!9LT

-mode

9sage: -mode hard coded modeefault: not used.

(t indicates that tIcoffee will use some hard coded parameters. These include*

3uic,aln* very fast appro@imate alignment

dali* a mode used to combine dali pairwise alignments

ealuate* defaults for evaluating an alignment

5dcoffee* runs tIcoffee with the 8dcoffee parameteriFation

ther modes e@ist that are not yet fully supported

-score [Deprecated]

9sage: -scoreefault: not used

Toggles on the evaluate mode and causes tIcoffee to evaluates a precomputed alignmentprovided via -infilealignmentB. The flag -outputmust be set to an appropriate format%i.e. -outputMscoreIascii, scoreIhtml or scoreIpdf'. $ better default parameteriFation isobtained when using the flag -modeealuate.

-evaluate

9sage: -ealuateefault: not used

2eplaces Zscore. This flag toggles on the evaluate mode and causes tIcoffee to evaluates a

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pre-computed alignment provided via -infilealignmentB. The flag -outputmust be set toan appropriate format %i.e. -outputMscoreIascii, scoreIhtml or scoreIpdf'.

The main purpose of Zevaluate is to let you control every aspect of the evaluation. Ket it isadvisable to use pre-defined parameteriFation* modeealuate.

PROMPT: t_coffee infile4sample_alnA.aln -mode4ealuate

PROMPT: t_coffee infile4sample_se,A.aln in 1sample_li(A.tc_li(mode4ealuate

-convert [cw]

9sage: -conertefault: turned off

Toggles on the conversion mode and causes T-Coffee to convert the se3uences, alignments,libraries or structures provided via the -infileand -inflags. The output format must be setvia the -outputflag. This flag can also be used if you simply want to compute a library %i.e.you have an alignment and you want to turn it into a library'.

This flag is Clustal) compliant.

-do_align [cw]

9sage: -do4alignefault: turned on

%>ecial $arameters

-version

9sage: -ersionefault: not used

2eturns the current version number

-proxy

9sage: -pro1ypro1yBefault: not used

5ets the pro@y used by 0TTPIpro@y $! httpIpro@y. 5etting with the propmpt supersedes$!K other setting.

!ote that if you use no pro@y, you should set

-pro@y

-email

9sage: -emailemailB

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efault: not used

5ets your email value as provided to web services

-check_configuration

9sage: -chec,4configurationefault: not used

Checks your system to determine whether all the programs T-Coffee can interact with areinstalled.

-cache

9sage: -cacheuse; update; ignore; filenameBBefault: -cac)e4use

4y default, tIcoffee stores in a cache directory, the results of computationally e@pensive%structural alignment' or network intensive %4L$5T search' operations.

-update

9sage: -updateefault: turned off

Causes a wgetaccess that checks whether the tIcoffee version you are using needs updating.

-full_log

9sage: -full4logfilenameB

efault: turned off

Causes tIcoffee to output a full log file that contains all the input&output files.

-plugins

9sage: -pluginsdirBefault: default

5pecifies the directory in which the companion packages %other multiple aligners used by #-Coffee, structural aligners, etcO' are kept as an alternative, you can also set the environmentvariable PLHG(!5I>ITC""AA

The default is N&.tIcoffee&plugins&

-other_pg

9sage: -other4pgfilenameBefault: turned off

5ome rumours claim that Tetris is embedded within T-Coffee and could be ran using somespecial set of commands. )e wish to deny these rumours, although we may admit thatseveral interesting reformatting programs are now embedded in tIcoffee and can be ranthrough the ZotherIpg flag.

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PROMPT: t_coffee ot)er_pg4se,_reformat

PROMPT: t_coffee ot)er_pg4unpacF_all

PROMPT: t_coffee ot)er_pg4unpacF_e"tract_from_pd(

&n>ut

%e"uence &n>ut

-infile [cw]

To remain compatible with Clustal), it is possible to indicate the se3uences with this flag

PROMPT: t_coffee -infile4sample_se,A.fasta

This flag sets the type of the se3uences. (f omitted, the type is guessed automatically. Thisflag is compatible with Clustal).

arnin: In case o lo% comple"it# or short seq!ences' it isrecommended to set the t#pe man!all#.

-se'

9sage: -se3JP;BnameB;Kefault: none

-se3 is now the recommended flag to provide your se3uences. (t behaves mostly likethe -in flag.

-se'_source9sage: -se34source!


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efault: 05J.

Kou may not want to combine all the provided se3uences into a single se3uence list. Kou cando by specifying that you do not want to treat all the Zin files as potential se3uence sources.

-se3IsourceMIL$ indicates that neither se3uences provided via the $ %$lignment' flag or via

the L %Library flag' should be added to the se3uence list.

-se3IsourceM5 means that only se3uences provided via the 5 tag will be considered. $ll theother se3uences will be ignored.

ut

-pdb

9sage: -pdbpdbid(B;pdbid2BJ#a1 2))K

efault: 5one

2eads or fetch a pdb file. (t is possible to specify a chain or even a sub-chain*

P%&!P%_6H0&5#Gopt !ut

-usetree

9sage: -usetreetree fileBefault: 5o file specified


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se3uences. Pre-compiled constraint list can also be proided. 'ach file proided

ia this flag must be preceded @ith a symbol Ddentifier T!GF that indicates its

nature to T-Coffee. The T!Gs currently supported are the follo@ing:

P P* structure

for se3uences Duse it as @ell to treat an #! as unaligned se3uencesF

# #ethods used to build the library

L Pre-computed T-Coffee library

! #ultiple !lignments that must be turned into a Library

ubstitution matrices.

& Profiles. This is a legal multiple alignments that @ill be treated as single

se3uences Dthe se3uences it contains @ill not be realignedF.

f you do not @ant to use the T!G; you @ill need to use the follo@ing flags inreplacement of -in. o not use the T!G @hen using these flags:

-aln !lignments D!F

-profile Profiles D&F

-method #ethod D#F

-se3 e3uences DF

-lib Libraries DLF

-in

9sage: -inJP;;!;L;#;BnameB;K

efault: -in4Mlalign_id_pairKMclustal8_pair

Note: -in can be replaced %ith the combined !sae o -aln' iprofle'.pdb' .lib' -method.

5ee the bo@ for an e@planation of the -in flag. The following argument passed via -in

PROMPT: t_coffee

-in4sample_se,A.fastaK0sample_alnA.alnK0sample_alnD.msfKMlalign_id_pairK1sample_li(A.tc_li( outfile4outaln

This command will trigger the following chain of events*

9-Gather all the se3uences

5e3uences within all the provided files are pooled together. "ormat recognition is automatic.uplicates are removed %if they have the same name'. uplicates in a single file are onlytolerated in "$5T$ format file, although they will cause se3uences to be renamed.

(n the above case, the total set of se3uences will be made of se3uences contained inse3uences9.se3, alignment9.aln, alignment.msf and library.lib, plus the se3uences initially

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gathered by -infile.

-Turn alignments into libraries

alignment9.aln and alignment.msf will be read and turned into libraries. $nother librarywill be produced by applying the method lalignIidIpair to the set of se3uences previouslyobtained %9'. The final library used for the alignment will be the combination of all this

information.

!ote as well the following rules*

(-%rder* The order in which se3uences, methods, alignments and libraries are fed in isirrelevant.

2-=eterogeneity* There is no need for each element %$, 5, L' to contain the same se3uences.

5-


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$rofile &n>ut

-profile

9sage: -profileJnameB;K ma1imum of 2)) profiles.

efault: no default

This flag causes T-Coffee to treat multiple alignments as a single se3uences, thus making itpossible to make multiple profile alignments. The profile-profile alignment is controlled by-profileImode and -profileIcomparison. )hen provided with the -inflag, profiles must be

preceded with the letter 2.

PROMPT: t_coffee profile sample_alnA.alnKsample_alnD.aln outfile4profile_aln

PROMPT: t_coffee inRsample_alnA.alnKRsample_alnD.alnKMslo8_pairKMlalign_id_pair

outfile4profile_aln

!ote that when using ZtemplateIfile, the program will also look for the templates associatedwith the profiles, even if the profiles have been provided as templates themselves %howeverit will not look for the template of the profile templates of the profile templatesO'

-profile( [cw]

9sage: -profile(JnameBK; one name onlyefault: no default

5imilar to the previous one and was provided for compatibility with Clustal).

-profile) [cw]

9sage: -profile(JnameBK; one name onlyefault: no default

5imilar to the previous one and was provided for compatibility with Clustal).

*li!nment Com>utation

i:rary Com>utation? ethos

-lalign_n_top

9sage: -lalign4n4topntegerBefault: -lalign_n_top4A2

!umber of alignment reported by the local method %lalign'.

-align_pdb_param_file

Hnsuported

-align_pdb_h

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