5.3 years ago by
needle takes two files as input. First file contains sequence to be aligned to the sequence or sequences in the second file. The first file can contain only one sequence and the second file can contain multiple sequences and needle will align the sequence from the first file to every sequence in the second file. Now coming to your question:
"filter" option only lets you to give the first sequence as a standard input. Here you are giving both the sequences as a standard input and as a result needle is not being able to detect the second input.
You can try:
needle "cat seq1.fasta |" "cat seq.2fasta |"