T-Coffee and related packages documentation (www.tcoffee.org)

Contents:

• T-Coffee Installation
  • Installation
    • Unix/Linux Binaries
    • MacOS Binaries - Updated
    • Installation From Source/Binaries downloader (Mac OSX/Linux)
  • Template based modes: PSI/TM-Coffee and Expresso
    • Why do I need BLAST with T-Coffee?
    • Using a BLAST local version on Unix
    • Using the EBI BLAST client
    • Using the NCBI BLAST client
    • Using another client
  • Troubleshooting
    • Third party packages
    • M-Coffee parameters
    • Structural modes (using PDB)
    • R-Coffee associated packages
• Quick Start Regressive Algorithm
  • Introduction
  • Installation from source
  • Examples
    • Fast and accurate
    • Slower and more accurate
    • Very Fast
  • Regressive flags
• Quick Start Unistrap
  • Introduction
  • Examples
    • Produce bootsrap replicates by shuffling sequences and guide tree sister nodes
    • Produce bootsrap replicates by shuffling the guide tree sister nodes
    • Get list of supported methods
  • unistrap flags
• Quick Start T-Coffee
  • Basic Command Lines (or modes)
    • Protein sequences
    • DNA sequences
    • RNA sequences
  • Brief Overview of T-Coffee Tools
    • Alignment methods
      • T-Coffee
      • M-Coffee
      • Expresso
      • R-Coffee
      • Pro-Coffee
    • Evaluation tools
      • TCS (MSA evaluation based on consistency)
      • iRMSD/APDB (MSA structural evaluation)
      • STRIKE (single structure MSA evaluation)
      • T-RMSD (structural clustering)
  • Tutorial (Practical Examples)
    • Introduction
    • Materials
    • Procedures
• T-Coffee Main Documentation
  • Before You Start…
    • Foreword
    • Prerequisite for using T-Coffee
    • Let’s have a try…
  • What is T-Coffee ?
    • What is T-Coffee?
      • What does it do?
      • What can it align?
      • How can I use it?
      • Is there an online webserver?
      • Is T-Coffee different from ClustalW?
      • Is T-Coffee very accurate?
    • What T-Coffee can and cannot do for you …
      • What T-Coffee can’t do
      • What T-Coffee can do
    • How does T-Coffee alignment works?
  • Preparing Your Data
    • The reformatting utility: seq_reformat
      • General introduction
      • Modification options
      • Using a “cache” file
        • What is a cache in T-Coffee?
        • Preparing a sequence/alignment cache
        • Preparing a library cache
    • Modifying the format of your data
      • Keeping/Protecting your sequence names
      • Changing the sequence format
      • Changing the case
        • Changing the case of your sequences
        • Changing the case of specific residues
        • Changing the case with a cache
      • Coloring/Editing residues in an alignment
        • Changing the default colors
        • Coloring specific types of residues/nucleic acids
        • Coloring a specific residue of a specific sequence
        • Coloring according to the conservation
        • Coloring an alignment using a cache
    • Modifying the data itself…
      • Modifiying sequences in your dataset
        • Converting residues
        • Extracting sequences according to a pattern
        • Extracting/Removing specific sequences by names
        • Extracting the most informative sequences
        • Extracting/Removing sequences with the % identity
        • Chaining important sequences
      • Modifying columns/blocks in your dataset
        • Removing gapped columns
        • Extracting specific columns
        • Extracting entire blocks
        • Concatenating blocks or MSAs
    • Manipulating DNA sequences
      • Translating DNA sequences into protein sequences
      • Back-translation with the bona fide DNA sequences
      • Finding the bona fide sequences for the back-translation
    • Manipulating RNA Sequences
      • Producing a Stockholm output: adding predicted secondary structures
        • Producing/Adding a consensus structure
        • Adding a precomputed consensus structure to an alignment
      • Analyzing a RNAalifold secondary structure prediction
        • Visualizing compensatory mutations
        • Analyzing matching columns
      • Comparing alternative folds
    • Phylogenetic Trees Manipulation
      • Producing phylogenetic trees
      • Comparing two phylogenetic trees
      • Scanning phylogenetic trees
      • Pruning phylogenetic trees
      • Tree Reformatting for MAFFT
    • Manipulating structure files (PDB)
      • Extracting a structure
      • Adapting extract_from_pdb to your own environment
  • Aligning Your Sequences
    • General comments on alignments and aligners
      • What is a good alignment?
      • The main methods and their scope
        • ClustalW is really everywhere…
        • MAFFT/MUSCLE to align big datasets
        • T-Coffee/ProbCons, slow but accurate !!!
      • Choosing the right package (without flipping a coin !)
    • Protein Sequences
      • General considerations
      • Computing a simple MSA (default T-Coffee)
      • Aligning multiple datasets/Combining multiple MSAs
      • Estimating the diversity in your alignment
      • Comparing alternative alignments
      • Comparing subsets of alternative alignments
      • Modifying the default parameters of T-Coffee
        • Can you guess the optimal parameters?
        • Changing the substitution matrix
        • Changing gap penalties
        • Aligning (very) large datasets
    • Protein sequences using 2D and/or 3D information
      • Using 3D structures: Expresso/3D-Coffee
        • Requirements to run Expresso/3D-Coffee
        • How does Expresso/3D-Coffee work?
        • Running Expresso/3D-Coffee
        • Template search paramaters
      • Aligning sequences and structures
        • Mixing sequence profile and structure templates
        • Aligning profile using structural information
      • Using secondary structure predictions
        • Single sequence prediction
        • Incorporation of the prediction in the alignment
        • Using other secondary structure predictions
        • Output of the prediction
    • RNA sequences using 2D and 3D Structure
      • RNA sequences using 2D structure (R-Coffee)
        • Introduction
        • R-Coffee: aligning RNA sequences using secondary structures
        • Improving R-Coffee
      • RNA Sequences using 2D and 3D structures (SARA-Coffee and RSAP-Coffee)
        • Running SARA/RSAP-Coffee
        • Estimating the accuracy of an RNA structure based alignment
        • Installing SARA-Coffee VM
        • Docker image for SARA-Coffee
    • Aligning DNA sequences
      • Aligning DNA sequences
      • Pro-Coffee: Aligning functional DNA regions
      • Splice variants
      • Noisy coding DNA sequences…
    • Using many MSA methods at once
      • Using third party aligner via T-Coffee
      • Using all the methods at the same time: M-Coffee
      • Using selected methods to compute your MSA
    • Aligning profiles
      • Aligning sequence(s) to profile(s)
      • Computing very accurate (but slow) alignments with PSI/TM-Coffee
  • Evaluating Your Alignment
    • Sequence Based Methods
      • The CORE index
        • Computing the local CORE index
        • Computing the CORE index of any alignment
      • Transitive Consistency Score (TCS)
        • Evaluating an existing MSA
        • Filtering unreliable MSA positions
        • Weighting MSA for improved trees
        • Using different libraries for TCS
        • Working with coding DNA
        • Summary of the output options
    • Structural evaluation of MSAs
      • APDB/iRMSD
        • What is the APDB/iRMSD?
        • How to efficiently use structural information?
        • Evaluating an alignment with the iRMSD package
        • Evaluating alternative alignments
        • DEC - Distance Evolutionnary Conservation with msa2distances
      • STRIKE: Contact based evaluations
    • Evaluating a MSA according to your own criterion
  • Downstream Analysis
    • Contact Evaluations
      • Contact Evaluation on proteins
    • Clustering/Trees based on protein 3D structures
      • Generating a tree based on 3D intramolecular distances conservation
      • Generating a tree based on contact conservation
      • Visualizing contact/distance conservation
      • Visualizing informative positions
      • Evaluating clustering capacities (under maintenance…)
      • Structural Tree Parameters
    • The T-RMSD
      • What is the T-RMSD?
      • Generating a structural tree with support values
      • Visualizing the structural clustering
    • The TCS
  • Internal/External Methods
    • What are the methods already integrated in T-Coffee?
      • INTERNAL methods (built-in)
      • EXTERNAL methods (plug-in)
    • Modifying the parameters of INTERNAL/EXTERNAL methods
      • Internal methods
      • External methods
    • Integrating EXTERNAL methods
      • Accessing external methods
      • Customizing an external method
      • Advanced method integration
      • The mother of all method files…
      • Weighting your method
      • Managing a collection of method files
    • Creating your own T-Coffee libraries
      • Using precomputed alignments
      • Customizing the weighting scheme
      • Generating your own libraries
    • Plug-out: using T-Coffee as a plug-in
• T-Coffee Technical Documentation
  • T-Coffee Parameters & Flags
    • T-Coffee general information
      • General syntax
      • T-Coffee flags
      • Setting up the parameters
      • Setting up the variables
      • CPU control
        • Multithreading
        • Limits
      • Meta-parameters
        • Global parameters
        • Misc parameters
        • Verbose parameters
    • Input(s)
      • The “-in” flag
      • Sequence input flags
      • Other input flags (structure, tree, profile)
    • Output(s)
      • Output files, format & names
      • Evaluation files
      • Alignments
      • Librairies & trees
    • Alignment Computation
      • Library computation: methods and extension
      • Tree computation
      • Weighting schemes
      • Pairwise alignment computation
      • Multiple alignment computation
      • Large scale aligment computation [Unsupported]
      • Local alignments computation [Unsupported]
      • Alignment post-processing
    • Template based modes
      • Database searches parameters
      • PSI-Coffee and TM-Coffee parameters
      • Using structures
      • Using/finding PDB templates for the sequences
      • Using structure for MSA evaluation
  • T-Coffee Parameter Files Format
    • Sequence name handling
    • Automatic format recognition
    • Libraries
      • T-COFFEE_LIB_FORMAT_01
      • T-COFFEE_LIB_FORMAT_02
      • Library List
    • Substitution matrices
      • BLAST format [Recommended]
      • ClustalW style [Deprecated]
    • Sequences weights
    • Parameter files
  • Technical Notes
    • Building a T-Coffee server
      • Environment Variables
      • Output of the .dnd file.
      • Permissions
      • Other Programs
    • Known Problems
    • Development
  • T-Coffee Test
    • Introducing a new command to test
    • Checking the documentation
    • Compiling the documentation
    • Making a new release
• T-Coffee Web Server
  • General
  • T-Coffee Simple MSA
  • Protein Sequences
    • Expresso (using 3D structures)
    • M-Coffee (combining multiple methods)
    • PSI/TM-Coffee (transmembrane proteins)
    • PSI-Coffee (homology extension)
  • RNA Sequences
    • R-Coffee (using 2D prediction)
    • SARA-Coffee (using 3D structures)
    • RM-Coffee (combining multiple methods)
  • DNA Sequences
    • M-Coffee (combining multiple methods)
    • Pro-Coffee (homologous promoter regions)
  • Evaluation Tools
    • TCS (Transitive Consistency Score)
    • iRMSD/APDB (MSA structural evaluation) (under maintenance…)
    • T-RMSD (structural clustering)
    • STRIKE (MSA evaluation with single structure)
• FAQ
  • Abnormal Terminations & 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: The program is crashing
    • Q: I am running out of memory
  • Input/Output control
    • Q: How many sequences can T_Coffee handle?
    • Q: Can I change line length in the defaut format?
    • 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?
    • Q: Is it possible to pipe stuff into T_Coffee?
    • Q: Can I read my parameters from a file?
    • Q: I want to decide myself on the name of the output files !!!
    • Q: I want to use the sequences in an alignment file
    • Q: I only want to produce a library
    • Q: I want to turn an alignment into a library
    • Q: I want to concatenate two libraries
    • Q: What happens to the gaps when an alignment is fed to T-Coffee?
    • Q: I cannot print the html graphic display!!!
    • Q: I want to output an html file and a regular file
    • Q: I would like to output more than one alignment format at the same time
  • Alignment computation
    • Q: Is T-Coffee the best? Why not using MUSCLE, MAFFT, or ProbCons???
    • Q: Can T_Coffee align nucleic acids ???
    • Q: I do not want to compute the alignment
    • Q: I would like to force some residues to be aligned
    • Q: I would like to use structural alignments
    • Q: I want to build my own libraries
    • Q: I want to use my own tree
    • Q: I want to align coding DNA
    • Q: I do not want to use all the possible pairs when computing the library
    • Q: I only want to use specific pairs to compute the library
    • Q: There are duplicates or quasi-duplicates in my set.
  • Using Structures and Profiles
    • Q: Can I align sequences to a profile with T-Coffee?
    • Q: Can I align sequences two or more profiles?
    • Q: Can I align two profiles according to the structures they contain?
    • Q: T-Coffee becomes very slow when combining sequences and structures
    • Q: Can I use a local installation of PDB?
  • Improving/Evaluating Your MSAs
    • Q: How can I edit my alignment manually?
    • Q: Have I improved or not my alignment?
    • Q: How good is my alignment?
    • Q: What is that color index?
    • Q: Can I evaluate alignments NOT produced with T-Coffee?
    • Q: Can I compare two alignments?
    • Q: I am aligning sequences with long regions of very good overlap
    • Q: Why is T-Coffee changing the names of my sequences!!!!
  • Release Notes
• T-Coffee release guide
  • Introduction
  • Making a new release
    • Beta Release
    • Stable Release
    • Major Release
  • Release Building Procedure
    • Triggering a release
    • CircleCI building
    • Publication
    • Using doc2test.pl
    • Compiling tests from the rst documentation
    • Compiling tests commands
    • Creating a new command to be tested
• Release Notes
• Citations & References
  • Comparative Genomics & Biology
  • T-Coffee Alignment Methods
  • T-Coffee Web Servers
  • T-Coffee Tools For MSA Evaluation
  • Reviews, Briefings & Books
• Contacts, Adresses & Contributions
  • Contact us
  • Adresses
  • Contributions
    • Main Contributions
    • Other Contributions
      • Softwares
      • Bug reports and feedback
• License & Terms of Use