T-Coffee and related packages documentation (www.tcoffee.org)¶
Contents:
- T-Coffee Installation
- Quick Start Regressive Algorithm
- Quick Start
- T-Coffee Main Documentation
- Before You Start…
- What is T-Coffee ?
- Preparing Your Data
- The reformatting utility: seq_reformat
- Modifying the format of your data
- Modifying the data itself…
- Manipulating DNA sequences
- Manipulating RNA Sequences
- Phylogenetic Trees Manipulation
- Manipulating structure files (PDB)
- Aligning Your Sequences
- General comments on alignments and aligners
- Computing simple MSA with T-Coffee
- Aligning (very) large datasets
- Using many methods at once
- Aligning profiles
- Using protein 2D/3D structural information
- Aligning RNA sequences
- Aligning DNA sequences
- Evaluating Your Alignment
- Downstream Analysis
- Internal/External Methods
- T-Coffee Technical Documentation
- T-Coffee Web Server
- FAQ
- Abnormal Terminations & Results
- Input/Output control
- Q: How many sequences can T_Coffee handle? [Deprecated]
- 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
- 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
- Citations & References
- Contacts, Adresses & Contributions
- License & Terms of Use