I have a transmembrane protein dataset, for which I want to use psicoffee for alignment. After browsing and digging around, I came up with the command:
t_coffee Pl-B2_s5_cdh70.fsa -mode psicoffee -blast_server LOCAL -protein_db /home/fer/Desktop/test/uniref90_TM/uniref90_TM.fasta
INPUT FILES
	Input File (M) proba_pair 
	Input File (S) Pl-B2_s5_cdh70.fsa  Format fasta_seq
Identify Master Sequences [no]:
Master Sequences Identified
Looking For Sequence Templates:
	Template Type: [BLAST] Mode Or File: [BLAST] [Start
#*****************************************************************
--ERROR: #  [FATAL:T-COFFEE]
# The Program 
legacy_blast.pl Needed by T-COFFEE Could not be found
# If 
legacy_blast.pl is installed on your system:
#
	     -Make sure 
legacy_blast.pl is in your $path:
# If 
legacy_blast.pl is NOT installed obtain a copy from:
#
	ftp://ftp.ncbi.nih.gov/blast/executables/LATEST#
#
# and install it manualy
******************************************************************
*************************************************************************************************
*                        FULL TRACE BACK PID: 46977                                    
46977 -- ERROR: #  [FATAL:T-COFFEE]
46977 -- COM: t_coffee Pl-B2_s5_cdh70.fsa -mode psicoffee -blast_server LOCAL -protein_db /home/fer/Desktop/test/uniref90_TM/uniref90_TM.fasta 
46977 -- STACK: 46930 -> 46977
*************************************************************************************************
# TERMINATION STATUS: FAILURE [PROGRAM: T-COFFEE pid 46977 ppid 46930
#CL: t_coffee Pl-B2_s5_cdh70.fsa -mode psicoffee -blast_server LOCAL -protein_db /home/fer/Desktop/test/uniref90_TM/uniref90_TM.fasta
I have already manually installed the package containing 
legacy_blast.pl, which I have also added to $PATH (I checked and it's dicoverable). Also, the database was formatted with makeblastdb.