List of alignment file formats accepted by TITO:

MSF multi-sequence format used by GCG 8.0/9.0 software (Keyword ALIMSF in the input filename of the alignment)
MUL for a MSF file from Multalin (Keyword ALIMUL in the input filename of the alignment)
MAT for a MSF file from MatchBoxin (Keyword ALIMAT in the input filename of the alignment)
PIR for a PIR file format (Keyword ALIPIR in the input filename of the alignment)
MAS for an alignment edited by the program SEAVIEW (Keyword ALIMAS in the input filename of the alignment)
FAS for a FASTA file format (Keyword ALIFAS in the input filename of the alignment)
CLU for an alignment from ClustalW (Keyword ALICLU in the input filename of the alignment)

List of (Alignment) Files from web servers and softwares accepted by TITO:

3DPSSM (Keyword ALI3DP in the input filename of the alignment)
PSI-BLAST (Keyword ALIPSI in the input filename of the alignment)
mGenThreader (Keyword ALIMGT in the input filename of the alignment)
HMMer (Keyword ALIHMM in the input filename of the alignment)
INBGU (Keyword ALIGBU in the input filename of the alignment)
NPSA (Keyword ALINPS in the input filename of the alignment)
MPSA (Keyword ALIMPS in the input filename of the alignment)