@ECHO OFF

> usermessage.vbs ECHO Set wshShell = CreateObject( "WScript.Shell" )
>>usermessage.vbs ECHO wshShell.Popup "Multiple Sequence Alingnment Started ... (It might take several minutes to complete depending on the size of the sequences.)", 20, "CaseIt! Message", 64

WSCRIPT.EXE usermessage.vbs
DEL usermessage.vbs

clustalw /align /type=protein /infile=MEGA4.fasta /output=fasta /outfile=out.fasta >z
clustalw /tree /infile=out.fasta > z
del z

> usermessage.vbs ECHO Set wshShell = CreateObject( "WScript.Shell" )
>>usermessage.vbs ECHO wshShell.Popup "Multiple Sequence Alingnment Done!!", 5, "CaseIt! Message", 64

WSCRIPT.EXE usermessage.vbs
DEL usermessage.vbs

@rem sed "s/>/#/g" out.fasta >out.tmp
@rem type megaheader.txt out.tmp > out.meg

REM del out.*

del tree.nwk
rename out.ph tree.nwk

start mega4.exe tree.nwk
start mega4.exe out.fasta
@rem start mega4.exe out.meg
