Please forgive me if I don't ask my question with the correct terms/syntax/etc.; I am in an introduction to bioinformatics class so this is all still very new to me given that I've had no experience with computers in this way whatsoever (have never even opened a terminal until this class).
I am having issues with the ClustalW program. I am running version 1.82. I am using PuTTY on a Windows computer.
I keep getting the error:
ERROR: Could not open sequence file INFILE=1P30Sr.faaGbl
This is what I'm running (it's actually in a bash script, but I get the same error in the command line): clustalw INFILE=1P30Sr.faaGbl -bootstrap=1000 -output=tree-CLW_1P30Sr.faaGbl -tree
This file is in fasta format (conversion to phylip did not fix anyway). My script does not look any different than fellow classmates' but theirs works and mine does not.
Can anyone please help me figure out why this is happening? I realize this is very simple, basic bioinformatics, but search engines did not help me find a resolution. The help flag also does not work for me for ClustalW (gives same error "cannot open help file"). I have used ClustalW before for alignments instead of trees, and it worked just fine.