Varies result while input FASTA vs STDIN FASTA

[anilthanki]

Hi

We are running T-Coffee heavily for our (GeneSeqToFamily) workflow and we found possibly a bug in T-Coffee. When we put same input (protein) FASTA file in different way

1. by using normal input file and (./t_coffee 'temp' -method clustalw_msa -output fasta_aln > direct.fasta)
2. by standard input (stdin), (cat temp | ./t_coffee '-infile=stdin' -method clustalw_msa -output fasta_aln > indirect.fasta)

resulting alignment varies.

I am attaching input and output files for your reference.

Archive.zip