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Software


Contents:

  1. Download
  2. Installation
  3. Methods distributed with SARSE
  4. Other methods
  5. Other editors

1. Download

Version 1.37 (2007-10-25)
Complete package: sarse-1.37.tar.gz

2. Installation

Refer to installation instructions in sarse/doc/install.txt


3. Methods distributed with SARSE

This is the programs that are distributed with SARSE. They are not all visible through the Tools/Programs menu but all the programs are usable from the command-line. There are also some format converters that makes it possiple to communicate with other programs.

pipes

  • pfold.pipe
  • pcluster.pipe
  • foldalignM.pipe

Pfold package

standard pfold:
  • maketree
  • scfg
pcluster:
  • cluster.tcsh
  • makestruc.tcsh
  • makeplots.tcsh
  • scfg
  • fasta2col

FoldalignM package

  • cluster.tcsh
  • pclusteranalysis
  • makeplots
  • fasta2col_groups
  • groupshade

RNAdbtools package

cleanup: coloring: formats: plotting: seqtools:

4. Other methods

The table below is provided as a suggestion to what programs could be integrated in SARSE. Please send updates to this list to info@sarse.ku.dk.

Algorithms
Version
Update
Platforms
Tools for communication
Alifold


col2fasta - ct2col
ClustalW


aln2txt - col2fasta
RNA-decoder



rdc2col - col2rdc
Mfold


ct2col
Sfold


ct2col
Vienna Package



CMfinder




5. Other editors

The table below is provided to give an overview of other RNA alignment and structure editors available. Please send updates to this list to info@sarse.ku.dk.

Alignment editors
Version
Update
Platforms
Tools for communication
ARB
2004 Linux col2fasta - fasta2col
BioEdit

Win
col2fasta - fasta2col
Jalview
1997 Java col2fasta
Belvue




XRNA



S2S
200506 Linux/Mac col2rnaml
SeqPup
2004 Mac
RALEE
2004 Linux Emacs
Se-Al v2.0a11 1999 Java
ConStruct v.2.0 1999 Win/Linux
ALE
Dead

Linux Emacs

2D editors




Rnaviz


col2ali - col2alis - col2ct
S2S



XRNA

Java col2mas
3D editors




S2S



ERNA3D
1997

3DNA



Pymol




Comments, questions, etc., email webmaster@sarse.ku.dk.


Last updated November 5th, 2007 by E. S. Andersen, A. Lind-Thomsen and J. Gorodkin