|
.T-coffee Tutorial |
Centre National De LA Recherche
scientifique
CENTRO DE REGULACCIO GENOMICA,
Cédric Notredame
www.tcoffee.org
T-Coffee:
Cheat Sheet
Tutorial and FAQ
T-Coffee Tutorial
(Version 6.18, August 2008)
T-Coffee, PSI-Coffee
3D-Coffee/Expresso
M-Coffee
R-Coffee
APDB and iRMSD
ă Cédric Notredame, Centro de Regulaccio Genomica and Centre National
de la Recherche
Getting the Example Files of the Tutorial
Is T-Coffee different from ClustalW?
What T-Coffee Can and Cannot do for you …
Combining Sequences and Structures
Identifying Occurrences of a Motif: Mocca
Preparing Your Data: Reformatting and Trimming With
seq_reformat
Accessing the T-Coffee Reformatting Utility
Dealing with Non-automatically recognized formats
Removing the gaps from an alignment
Changing the case of your sequences
Changing the case of specific residues
Changing the case depending on the score
Protecting Important Sequence Names
Colouring/Editing Residues in an Alignment
Coloring specific types of residues
Coloring a specific residue of a specific sequence
Coloring according to the conservation
Colouring/Editing residues in an Alignment Using a Cache
Preparing a Sequence or Alignment Cache
Coloring an Alignment using a cache
Evaluating an alignment and producing a cache
Evaluating an alignment with T-Coffee
Evaluating the level of conservation with a substitution
matrix
Selectively turn some residues to lower case
Selectively modifying residues
Keeping only the best portion of an alignment
Extracting Portions of Dataset
Extracting The High Scoring Blocks
Extracting Sequences According to a Pattern
Extracting Blocks Within Alignment
Analyzing your Multiple Sequence Alignment
Estimating the diversity in your alignment
Reducing and improving your dataset
Extracting the N most informative sequences
Extracting all the sequences less than X% identical
Forcing Specific Sequences to be kept
Identifying and Removing Outlayers
Translating DNA sequences into Proteins
Back-Translation With the Bona-Fide DNA sequences
Finding the Bona-Fide Sequences for the Back-Translation
Guessing Your Back Translation
Fetching The Sequence of a PDB structure
Adapting extract_from_pdb to your own environment
Manipulating RNA sequences with seq_reformat
Producing a Stockholm output: adding predicted secondary
structures
Producing a consensus structure
Adding a consensus structure to an alignment
Analyzing an alifold secondary structure prediction
Visualizing compensatory mutations
Manipulating Phylogenetic Trees with seq_reformat
Comparing two phylogenetic trees
Building Multiple Sequence Alignments
How to generate The Alignment You Need?
The Main Methods and their Scope
Computing Multiple Sequence Alignments With T-Coffee
Computing Very accurate (but slow) alignments with
PSI-Coffee
A Simple Multiple Sequence Alignment
Aligning Very Large Datasets with Muscle
Aligning Very Large Alignments with Mafft
Aligning Very Large Alignments with T-Coffee
Shrinking Large Alignments With T-Coffee
Modifying the default parameters of T-Coffee
Changing the Substitution Matrix
Comparing Two Alternative Alignments
Can You Guess The Optimal Parameters?
Using All the Methods at the Same Time: M-Coffee
Using Selected Methods to Compute your MSA
Combining pre-Computed Alignments
Aligning One sequence to a Profile
Aligning Many Sequences to a Profile
Aligning Other Types of Sequences
Using Secondary Structure Predictions:
Incorporation of the prediction in the alignment
Using other secondary structure predictions
Combining Sequences and 3D-Structures
If you are in a Hurry: Expresso
Aligning Sequences and Structures
Mixing Sequences and Structures
Aligning Profile using Structural Information
Evaluating Alignments with The CORE index
Computing the Local CORE Index
Computing the CORE index of any alignment
Evaluating an Alignment Using Structural Information:
APDB and iRMSD
How to Efficiently Use Structural Information
Evaluating an Alignment With the iRMSD Package
Evaluating Alternative Alignments
Identifying the most distantly related sequences in your
dataset
Evaluating an Alignment according to your own Criterion
Establishing Your Own Criterion
Integrating External Methods In T-Coffee
What Are The Methods Already Integrated in T-Coffee
Plug-In: Using Methods Integrated in T-Coffee
Modifying the parameters of Internal and External Methods
Direct access to external methods
Customizing an external method (with parameters) for
T-Coffee
Managing a collection of method files
The Mother of All method files…
Plug-Out: Using T-Coffee as a Plug-In
Creating Your Own T-Coffee Libraries
Customizing the Weighting Scheme
Abnormal Terminations and Wrong Results
Q: The
program keeps crashing when I give my sequences
Q: The
default alignment is not good enough
Q: The
alignment contains obvious mistakes
Q: How
many Sequences can t_coffee handle
Q: Can I
prevent the Output of all the warnings?
Q: How
many ways to pass parameters to t_coffee?
Q: How
can I change the default output format?
Q: My
sequences are slightly different between all the alignments.
Q: Is it
possible to pipe stuff OUT of t_coffee?