Tehdyt toimenpiteet
MAFFT at CSC
Version
MAFFT 6.853is available in Hippu and in Embster graphical sequence analysis interface
MAFFT 6.811 is available in Vuori
MAFFT 6.708 is available in Murska
Description
MAFFT is a fast and accurate multiple sequence alignment program for protein and nucleotide sequences. MAFFT offers several different alignment strategies from which user should select the most suitable for his case.
Usage
Graphical interface for MAFFT is available in Embster platform
To set up the MAFFT commands in Hippu, Vuori or Murska, give command :
module load mafft
After this you can use MAFFT with command syntax:
mafft --parametes input_file.fasta > aligned_output.fasta
The most commonly used alignment strategies have their own command aliases. Part of them are listed bellow:
- L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information)
mafft --localpair --maxiterate 1000 input > output
linsi input > output (Alias; works the same as the above)
- G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information):
mafft --globalpair --maxiterate 1000 input > output
ginsi input > output (Alias)
- E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences):
mafft --ep 0 --genafpair --maxiterate 1000 input > output
einsi input > output (Alias)
- Alignment of two alignments
mafft-profile group1 group2 > output
Help
More detailed information about the program is available in the MAFFT home page.
| Mattila Kimmo | Kimmo.Mattila at csc.fi |
| Saren Ari-Matti | Ari-Matti.Saren at csc.fi |
