2. New to this version

Information on previous versions follows the program descriptions. See Section 11.4.

2.1 Version 3.0

October 1999

• The SAM-T99 iterative method for remote homology detection. This is the vastly preferred method for building an HMM from a single protein sequence and for weighting sequences when an alignment is available. See Section 4 and Section 9.4.3.

• Inclusion of the view_pdoc program for viewing the posterior decoded alignment. This may assist in checking alternate paths in an alignment. See Section 10.4.

• The uniqueseq program can now be used on alignments to eliminate sequences that match other sequences in the alignment. See Section 10.8.5.

• The hmmscore program will calculate E-values for reverse-sequence null model scoring (scores better than 1e-300 are reported as 1e-300). Internal Z-scoring has been eliminated. Score data can be output in the RDB format. See Section 10.2.

• Also in hmmscore, the reverse null model is now the default null model calculation. This doubles runtime over the simple null model, but is more accurate. To reduce this cost, set simple_threshold to -10, which means that only sequences that score better than this threshold will have the reverse null model score calculated. See Section 10.2.

• The default null model (as well as all FIMs) now includes by default a self-loop transition probability equal to the geometric average of the match to match transitions in the HMM (fimtrans is 1.0). The way in which insert to insert arcs are set for negative values of fimtrans has changed. See Section 8.5.

• Regardless of input format, selected sequence output is always in FASTA format. Sequence annotation lines are now preserved in sequence output files (sel, a2m, and mult files), and are truncated to the first 50 characters in dist and mstat files.

• In buildmodel, constrained trainining is now supported. Specific residues can be constrained to specific model nodes during training. This serves as a method of incorporation prior knowledge about the training sequence, such as structurally similar regions. See Section 9.6.

• The buildmodel seed parameter has been renamed randseed to avoid confusion with the SAM-T99 seed alignment parameter.