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eli1
March 4th, 2012, 05:04 AM
Hi,

I`m trying to do MSA by t_coffee in ubuntu. My multiple sequence file is result.fa that consists of 6 mt sequences. I dont know how to get phylogeny tree by t_coffee. Is there any body who can help me???

23dornot23d
March 4th, 2012, 05:19 AM
There is a program in the repos

https://www.google.com/search?q=ClustalX

sudo apt-get install clustalx

http://img40.imageshack.us/img40/4750/snapshot6dh.jpg

eli1
March 4th, 2012, 05:34 AM
There is a program in the repos

https://www.google.com/search?q=ClustalX


tanX 23dornot23d but this is not T-Coffee...I need to get phylogeny tree through this method. ](*,)

23dornot23d
March 4th, 2012, 06:12 AM
You did check the wiki out ...... http://en.wikipedia.org/wiki/T-Coffee



Comparisons with other alignment software

While the default output is a Clustal-like format, it is sufficiently different from the output of ClustalW/X that many programs supporting Clustal format cannot read it; fortunately ClustalX can import T-Coffee output so the simplest fix for this issue is usually to import T-Coffee's output into ClustalX and then re-export. Another possibility is to request the strict Clustalw output format with the option "-output=clustalw_aln".
An important specificity of T-Coffee is its ability to combine different methods and different data types. In its latest version, T-Coffee can be used to combine protein sequences and structures, RNA sequences and structures. It can also run and combine the output of the most common sequence and structure alignment packages. For a complete list see: tclinkdb.txt (http://www.tcoffee.org/Resources/tclinkdb.txt)
T-Coffee comes along with a sophisticated sequence reformatting utility named seq_reformat. An extensive documentation is available from t_coffee_technical.htm (http://www.tcoffee.org/Documentation/t_coffee/t_coffee_technical.htm) along with a tutorial t_coffee_tutorial.htm (http://www.tcoffee.org/Documentation/t_coffee/t_coffee_tutorial.htm)

Quote from T coffee tutorial .....



Producing phylogenetic trees

Seq_reformat is NOT a phylogeny package, yet over the time it has accumulated a few functions that make it possible to compute simple phylogenetic trees, or similar types of clustering:
Given a multiple sequence alignment, it is possible to compute either a UPGM or an NJ tree:
seq_reformat -in <aln> -action +aln2tree -output newick

Will use an identity matrix to compare your sequences and will output an unrooted NJ tree in newick format. If you want to produce a rooted UPGMA tree:
seq_reformat -in <aln> -action +aln2tree _TMODE_upgma -output newick

If your data is not data sequence, but a matrix of 1 and Os (i.e. SAR matrix for instance), you can use a different matrix to compute the pairwise distances:
seq_reformat -in <aln> -action +aln2tree _MATRIX_sarmat -output newick

All these parameters can be concatenated:
seq_reformat -in <aln> -action +aln2tree _TMODE_upgma_MATRIX_sarmat -output newick

Bootstrap facilities will also be added at some point … For now we recommend you use Phylip if you need some serious phylogeny…

http://code.google.com/p/tcoffee/source/browse/tcoffee/trunk/testsuite/all/server/.testcase?r=1152


http://spdbv.vital-it.ch/TheMolecularLevel/Matics/improve.html

This last link seems to be an online application ..... for it ....

http://tcoffee.vital-it.ch/cgi-bin/Tcoffee/tcoffee_cgi/index.cgi?stage1=1&daction=TCOFFEE::Regular