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The reason is some internal tagging being done by T-Coffee, with A for
Alignments and S for sequences. Normally, this should not interfere with
file names, but it not be well supported by the -infile flag.
The easiest fiy is to add the letter A before every filename provided
via -infile. If your file is name ASA.fasta, try:
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##########################################
Dr Cedric Notredame
Group Leader
Notredame's lab - Comparative Bioinformatics Group
Bioinformatics and Genomics Programme
Room 440.03
Centre de Regulació Genòmica (CRG)
Dr. Aiguader, 88
08003 Barcelona
Spain
To replicate the issue:
Release: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477)
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