Tehdyt toimenpiteet

Muscle

Version

Muscle v3.8.31 is available in Taito

Muscle v3.7 is available in Hippu

Muscle is a fast and accurate sequence alignment program. It's novelty lies in the algorithm that initially creates a fast and crude alignment that is subsequently refined to a more optimal alignment.

Usage

In Taito Muscle is taken in use with command:

module load biokit

In Hippu a set-up command is not needed.

A basic alignment from FastA-formatted input sequences (here, in file inseqs.fasta) is created by the call:

muscle -in inseqs.fasta -out outseqs.fasta

Note that the output is also in FastA format. If you need to get the alignment in, say, Phylip format, you first need to save the alignment in muscle in Clustal-format. Then you need to open and save this alignment in Clustal in Phylip format. Clustal-formatted alignments can be produced with the following command:

muscle -in inseqs.fasta -out outseqs.fasta -clw -clwstrict

Options related to refining and creation of large alignment are described in detail in the manual.

CSC

Osiot

Aliosiot

Tehdyt toimenpiteet

Muscle

Version

Description

Usage

Help

Reference

Distribution


Sisältö Biosciences Databases Courses and events Books and magazines Research and Development Networks Chemistry Computational Fluid Dynamics Earth science Electromagnetics Language research Mathematical modelling Nanoscience Numerical methods Physics Parallel computing Program development Statistics Structural analysis Visualization	Tehdyt toimenpiteet Muscle Version Muscle v3.8.31 is available in Taito Muscle v3.7 is available in Hippu Description Muscle is a fast and accurate sequence alignment program. It's novelty lies in the algorithm that initially creates a fast and crude alignment that is subsequently refined to a more optimal alignment. Usage In Taito Muscle is taken in use with command: module load biokit In Hippu a set-up command is not needed. A basic alignment from FastA-formatted input sequences (here, in file inseqs.fasta) is created by the call: `muscle -in inseqs.fasta -out outseqs.fasta` Note that the output is also in FastA format. If you need to get the alignment in, say, Phylip format, you first need to save the alignment in muscle in Clustal-format. Then you need to open and save this alignment in Clustal in Phylip format. Clustal-formatted alignments can be produced with the following command: `muscle -in inseqs.fasta -out outseqs.fasta -clw -clwstrict` Options related to refining and creation of large alignment are described in detail in the manual. Help More detailed information about the program is available in the manual. Reference Please site: Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5), 1792-97. Distribution You can download Muscle (UNIX, Linux, Windows) from it's website.