# REM 29 March 2010 K.Will. 
# 
# Simple script to do a series of ClustalW alignments and then make
# an alignment file for each parameter set and a single file that 
# includes all the alignments in one big matrix (elided). You must 
# have Clustalw2.exe and your input file in the directory with this 
# file.
# 
# Note: on a mac, the permissions for this batch file must be set to 
# executable.  E.g.:
# 1. type "ls -l" at the terminal
# 2. to make file executable, type "chmod u+x clustalwscrip_mac.bat"
# 3. type "ls -l" again to see that the permissions have changed for 
# user (who can now rwx, i.e. read write execute), but not for
# groups (g) or others
# 
# REM You must edit the input file name and the output files and 
# set all the parameters to what you want. This example does 14 
# different alignments, but you can make it as large or small as 
# you need. Keep -outorder=input. This is written for to produce Clustal 
# *.aln files. 
# 
# Run ClustalW
clustalw -infile=ray_seqs_all.fasta -outfile=ray_seqs_A_aln.aln -outorder=input -type=dna -PWGAPOPEN=22.50 -PWGAPEXT=9.99 -GAPOPEN=22.5 -GAPEXT=9.99 -ITERATION=alignment -NUMITER=100 -MAXDIV=40 -TRANSWEIGHT=0.5
clustalw -infile=ray_seqs_all.fasta -outfile=ray_seqs_B_aln.aln -outorder=input -type=dna -PWGAPOPEN=22.50 -PWGAPEXT=9.99 -GAPOPEN=22.5 -GAPEXT=9.99 -ITERATION=alignment -NUMITER=100 -MAXDIV=40 -TRANSWEIGHT=0.0
clustalw -infile=ray_seqs_all.fasta -outfile=ray_seqs_C_aln.aln -outorder=input -type=dna -PWGAPOPEN=18.75 -PWGAPEXT=8.33 -GAPOPEN=18.75 -GAPEXT=8.33 -ITERATION=alignment -NUMITER=100 -MAXDIV=40 -TRANSWEIGHT=0.5
clustalw -infile=ray_seqs_all.fasta -outfile=ray_seqs_D_aln.aln -outorder=input -type=dna -PWGAPOPEN=18.75 -PWGAPEXT=8.33 -GAPOPEN=18.75 -GAPEXT=8.33 -ITERATION=alignment -NUMITER=100 -MAXDIV=40 -TRANSWEIGHT=0.0
clustalw -infile=ray_seqs_all.fasta -outfile=ray_seqs_E_aln.aln -outorder=input -type=dna -PWGAPOPEN=15.00 -PWGAPEXT=6.66 -GAPOPEN=15.00 -GAPEXT=6.66 -ITERATION=alignment -NUMITER=100 -MAXDIV=40 -TRANSWEIGHT=0.5
clustalw -infile=ray_seqs_all.fasta -outfile=ray_seqs_F_aln.aln -outorder=input -type=dna -PWGAPOPEN=15.00 -PWGAPEXT=6.66 -GAPOPEN=15.00 -GAPEXT=6.66 -ITERATION=alignment -NUMITER=100 -MAXDIV=40 -TRANSWEIGHT=0.0
clustalw -infile=ray_seqs_all.fasta -outfile=ray_seqs_G_aln.aln -outorder=input -type=dna -PWGAPOPEN=11.25 -PWGAPEXT=5.00 -GAPOPEN=11.25 -GAPEXT=5.00 -ITERATION=alignment -NUMITER=100 -MAXDIV=40 -TRANSWEIGHT=0.5
clustalw -infile=ray_seqs_all.fasta -outfile=ray_seqs_H_aln.aln -outorder=input -type=dna -PWGAPOPEN=11.25 -PWGAPEXT=5.00 -GAPOPEN=11.25 -GAPEXT=5.00 -ITERATION=alignment -NUMITER=100 -MAXDIV=40 -TRANSWEIGHT=0.0
clustalw -infile=ray_seqs_all.fasta -outfile=ray_seqs_I_aln.aln -outorder=input -type=dna -PWGAPOPEN=7.50 -PWGAPEXT=3.33 -GAPOPEN=7.50 -GAPEXT=3.33 -ITERATION=alignment -NUMITER=100 -MAXDIV=40 -TRANSWEIGHT=0.5
clustalw -infile=ray_seqs_all.fasta -outfile=ray_seqs_J_aln.aln -outorder=input -type=dna -PWGAPOPEN=7.50 -PWGAPEXT=3.33 -GAPOPEN=7.50 -GAPEXT=3.33 -ITERATION=alignment -NUMITER=100 -MAXDIV=40 -TRANSWEIGHT=0.0
clustalw -infile=ray_seqs_all.fasta -outfile=ray_seqs_K_aln.aln -outorder=input -type=dna -PWGAPOPEN=6.57 -PWGAPEXT=2.50 -GAPOPEN=6.57 -GAPEXT=2.50 -ITERATION=alignment -NUMITER=100 -MAXDIV=40 -TRANSWEIGHT=0.5
clustalw -infile=ray_seqs_all.fasta -outfile=ray_seqs_L_aln.aln -outorder=input -type=dna -PWGAPOPEN=6.57 -PWGAPEXT=2.50 -GAPOPEN=6.57 -GAPEXT=2.50 -ITERATION=alignment -NUMITER=100 -MAXDIV=40 -TRANSWEIGHT=0.0
clustalw -infile=ray_seqs_all.fasta -outfile=ray_seqs_M_aln.aln -outorder=input -type=dna -PWGAPOPEN=5.63 -PWGAPEXT=1.67 -GAPOPEN=5.63 -GAPEXT=1.67 -ITERATION=alignment -NUMITER=100 -MAXDIV=40 -TRANSWEIGHT=0.5
clustalw -infile=ray_seqs_all.fasta -outfile=ray_seqs_N_aln.aln -outorder=input -type=dna -PWGAPOPEN=5.63 -PWGAPEXT=1.67 -GAPOPEN=5.63 -GAPEXT=1.67 -ITERATION=alignment -NUMITER=100 -MAXDIV=40 -TRANSWEIGHT=0.0
# 
# REM If the final output file exists this command will append data not 
# overwrite the file. You must edit the resulting file by searching for and
# removing the text "CLUSTAL 2.0.10 multiple sequence alignment" from all EXCEPT
# the first line in the file. open it in ClustalX and save as fasta or whatever. 
# 
cat *_aln.aln > elide.aln