Applications/Mafft - Revision history

Pysdlb: /* Batch Job */

2022-11-17T12:54:33Z

‎Batch Job

Pysdlb: /* Usage Examples */

2022-11-17T12:54:13Z

‎Usage Examples

Pysdlb: /* Application Details */ corrected details

2022-11-17T12:45:36Z

‎Application Details: corrected details

Pysdlb: /* Further Information */

2022-11-16T10:49:13Z

‎Further Information

Pysdlb: /* Navigation */

2022-11-16T10:49:06Z

‎Navigation

Pysdlb at 13:09, 24 May 2019

2019-05-24T13:09:00Z

Pysdlb at 14:12, 7 June 2018

2018-06-07T14:12:18Z

Pysdlb at 09:04, 3 May 2018

2018-05-03T09:04:50Z

Pysdlb: Created page with "TOC ==Application Details== * Description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. * Version: 2.2...."

2018-05-03T09:04:16Z

Created page with "__TOC__ ==Application Details== * Description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. * Version: 2.2...."

New page

__TOC__

==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===

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ module load 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)
@

</pre>

===Command line processing===

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ module load mafft/7.397
[username@login01 ~]$ mafft [arguments] input > output
</pre>

An alias for an accurate option (L-INS-i) for an alignment of up to ∼200 sequences × ∼2,000 sites:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ mafft-linsi input > output
</pre>

A fast option (FFT-NS-2) for a larger sequence alignment:

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ mafft input > output
</pre>

If not sure which option to use,

<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
[username@login01 ~]$ mafft --auto input > output
</pre>

---------------------------------------------------------------------

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)
@

</pre>

==Further Information==

* [https://mafft.cbrc.jp/alignment/software/ https://mafft.cbrc.jp/alignment/software/]
* [https://en.wikipedia.org/wiki/MAFFT https://en.wikipedia.org/wiki/MAFFT]

{|
|style="width:5%; border-width: 0" | [[File:icon_home.png]]
|style="width:95%; border-width: 0" |
* [[Main_Page|Home]]
* [[Applications|Application support]]
* [[General|General]]
* [[Training|Training]]
* [[Programming|Programming support]]
|-
|}

@@ Line 63: / Line 63: @@
 <!-- ty NIH: https://hpc.nih.gov/apps/mafft.html -->
 <pre>
 #SBATCH J mafftjob
 #SBATCH N 1

← Older revision		Revision as of 10:49, 16 November 2022
Line 67:		Line 67:


−	~~==Navigation==~~	+	{{Modulepagenav}}
−
−	* [[Main_Page\|Home]]
−	~~* [[Applications\|Application support]] *~~
−	* [[General\|General]]
−	* [[Programming\|Programming support]]

← Older revision		Revision as of 09:04, 3 May 2018
Line 60:		Line 60:
	</pre>		</pre>

−
−
−
−
−
−	~~---------------------------------------------------------------------~~
−
−	~~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)~~
−	@
−
−
−
−	~~</pre>~~

	==Further Information==		==Further Information==

@@ Line 59: / Line 59: @@
 [username@login01 ~]$ mafft --auto input > output
 </pre>
-−
 ==Further Information==

@@ Line 3: / Line 3: @@
 ==Application Details==
-* Description: Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
+* Description: MAFFT is used to  create multiple sequence alignments of amino acid or nucleotide sequences.
 * Version: 2.2.9 (compiled with gcc)
-* Modules: bowtie2/gcc/2.2.9
+* Modules: mafft/7.397
 * Licence: Open source (Github)
 ==Usage Examples==

@@ Line 65: / Line 65: @@
 * [https://mafft.cbrc.jp/alignment/software/ https://mafft.cbrc.jp/alignment/software/]
 * [https://en.wikipedia.org/wiki/MAFFT https://en.wikipedia.org/wiki/MAFFT]
 {{Modulepagenav}}

@@ Line 67: / Line 67: @@
-{|
+==Navigation==
-|style="width:5%; border-width: 0" | [[File:icon_home.png]]
 * [[Main_Page|Home]]
-* [[Applications|Application support]]
+* [[Applications|Application support]] *
 * [[General|General]]
 * [[Programming|Programming support]]

@@ Line 13: / Line 13: @@
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
-[username@login01 ~]$ module load mafft/7.397
+[username@login01 ~]$ module add mafft/7.397
 [username@login01 ~]$ mafft
@@ Line 35: / Line 35: @@
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
-[username@login01 ~]$ module load mafft/7.397
+[username@login01 ~]$ module add mafft/7.397
 [username@login01 ~]$ mafft [arguments] input > output
 </pre>