Difference between revisions of "Applications/Mafft"
From HPC
m |
m |
||
| Line 67: | Line 67: | ||
| − | + | ==Navigation== | |
| − | + | ||
| − | |||
* [[Main_Page|Home]] | * [[Main_Page|Home]] | ||
| − | * [[Applications|Application support]] | + | * [[Applications|Application support]] * |
* [[General|General]] | * [[General|General]] | ||
| − | |||
* [[Programming|Programming support]] | * [[Programming|Programming support]] | ||
| − | |||
| − | |||
Revision as of 13:09, 24 May 2019
Contents
Application Details
- Description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
- Version: 2.2.9 (compiled with gcc)
- Modules: bowtie2/gcc/2.2.9
- Licence: Open source (Github)
Usage Examples
Manual execution
[username@login01 ~]$ module add mafft/7.397
[username@login01 ~]$ mafft
---------------------------------------------------------------------
MAFFT v7.397 (2018/Apr/16)
MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)
https://mafft.cbrc.jp/alignment/software/
---------------------------------------------------------------------
Input file? (fasta format)
@
Command line processing
[username@login01 ~]$ module add mafft/7.397 [username@login01 ~]$ mafft [arguments] input > output
An alias for an accurate option (L-INS-i) for an alignment of up to ∼200 sequences × ∼2,000 sites:
[username@login01 ~]$ mafft-linsi input > output
A fast option (FFT-NS-2) for a larger sequence alignment:
[username@login01 ~]$ mafft input > output
If not sure which option to use,
[username@login01 ~]$ mafft --auto input > output
Further Information