Monday, 16 September 2019

HoKAlign

**** HoKAlign ****

*** A GUI under Windows for several free command line driven sequence alignment programs ***

 

 Currently supported alignment programs

  • ClustalW (GUI: ClustalX 2)
  • ClustalW2 (GUI: ClustalX 1)
  • Muscle (versions 3.6 and 3.7)
  • MAFFT (supported, the source for Cygwin is stored in the subfolder \scr - obsolete, now uses the Windows "All-in-one version")
  • T-Coffee
  • KAlign
  • DiAlign
  • Prank (GUI: Prankster)
  • ProbCons
  • Amap
  • ProDA
  • PCMA
  • POA

What you need in addition

  • obsolete - Cygwin (http://www.cygwin.com/ ) to run MAFFT
  • Java (http://www.java.com/ ) to run ReadSeq
  • ReadSeq is used for the conversion of the input files into the Fasta format and, if necessary, for the conversion of the output files into the MSF format. (not in use currently as ClustalW is used for the convert function)




  • GeneDoc (http://www.nrbsc.org/downloads/, March 2, 2007) to display the MSF output files. You can get the latest version 2.7.001 with the EXE-file form May 27, 2007 from here.
  • JalView (http://www.jalview.org/ ) to display the MSF output files
  • A file viewer or editor. Here is a short list of possibilities:

    • The folders

    • \ contains the compiled script (HoKAlign.exe) and the hokalign.ini file. Please adjust this ini-file according to your systems settings
    • \bin contains the executables (if possible compressed with UPX), and batch files
    • \doc contains available documentations for the alignment programs
    • \mat contains matrixes used by DiAlign
    • \pix contains pictures and icons
    • \scr contains the source for MAFFT under Cygwin
    • \seq contains example sequence files

    Internet sources for the programs used

    How to install

    • Unpack the files form the Zip file while keeping the folder structur. C:\Program Files\HoKAlign\ would be a good place.
    • Create a shortcut to the file HoKAlign.exe. Your desktop would be a good place to place this shortcut.
    • Java is necessary to run ReadSeq and ATV (Archaeopteryx). ReadSeq or ClustalX are used for all programs that can not read or write MSF files (e.g. Muscle). So you should have installed Java.
    • If you want to use MAFFT you must have installed Cygwin. After that you have to install the MAFFT package, stored in the /scr subfolder, as described here.

    Common known problems

    • The conversion from the GCG MSF format into the FASTA format with the help of ClustalW or ReadSeq does not work because the MSF file has a wrong format.
      Check with the editor (The E-button) the input MSF file. The first line of an MSF file should only contain "PileUP" (without the quotes).
    • Error messages, due to alpha stage. :)

    To do

    after
    • Version 0.2 alpha
      • Feature: The conversion form MSF to FASTA overwrites existing FASTA files. Temporary sequence (FASTA, MSF) files should be used for all the processes.
      • Update: of MAFFT to the Cygwin free All-in-one package for Windows
      • Update: of Muscle to version 3.8
      • Error: The program can be started without a sequence file when "Cancle" is pressed during the startup dialoge. This is not intendet.
      • Error: The last produced tree file may not be opened due to different file endings (dnd, ph, phb)
      • Feature: Check of errorlevel outputs to give feedback on run problems.
      • Feature: Implementation of ProDa
      • Feature: Implementation of Gblocks for block masking
      • Feature: Implementation of Clustal Omega
      • Feature: "Tree only" option
      • Feature: Implementation of FastTree
      • Feature: User selection of conversion with ClustalW or ReadSeq
    The program comes without any warrenties.
    Benutzung auf eigene Verantwortung.
    "As is" software.
    You have to accept the copyrights of all included programs.
    HoKAlign itself is freeware.

    Download

    Full package
    Update to version 0.3.1
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