How to run clustalw to generate a new phylogenetic tree based an old profile in command line?

Question

[User 1874]

0 down vote favorite I want to run clustalw non-interactively, i.e., with options

I have a fasta file with 10 sequences, named ten.fa, for which I generated alignment and phylogenetic tree, with command like:

name=ten clustalw2 -INFILE=$name.fa -ALIGN -OUTFILE=$name.aln clustalw2 -INFILE=$name.aln -TREE -OUTFILE=$name.ph so far I have following files

ten.fa ten.aln ten.ph

I have a new fasta file with 1 sequence, named

one.fa

for which I want to generate new aln and phylogenetic tree, named like

eleven.aln eleven.ph

How should I construct the command line? TIA

[goodez]

Maybe this will help (not meant to be rude I just don't have experience with this):

6) SUMMARY OF THE COMMAND LINE USAGE

Clustal W is designed to be run interactively. However, there are many situations where it is convenient to run it from the command line, especially if you wish to run it from another piece of software (e.g. SeqApp or GDE). All parameters can be set from the command line by giving options after the clustalw command. On UNIX options should be preceded by '-', all other systems use the '/' character.

If anything is put on the command line, the program will (attempt to) carry out whatever is requested and will exit. If you wish to use the command line to set some parameters and then go into interactive mode, use the command line switch: interactive .... e.g.

clustalw -quicktree -interactive on UNIX or

clustalw /quicktree /interactive on VMS,MAC and PC

will set the default initial alignment mode to fast/approximate and will then go to the main menu.

To see a list of all the command line parameters, type:

clustalw -options on UNIX or

clustalw /options on VMS,MAC and PC

and you will see a list with no explanation.

To get (VERY BRIEF) help on command line usage, use the /HELP or /CHECK (-help or -check on UNIX systems) options. Otherwise, the command line usage is self explanatory or is explained in clustalv.doc. The defaults for all parameters are set in the file param.h which can be changed easily (remember to recompile the program afterwards :-).

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