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       amap - Protein multiple alignment by sequence annealing


       amap [OPTION] [MFAFILE] [MFAFILE]


       AMAP is a tool to perform multiple alignment of peptidic sequences. It
       utilizes posterior decoding, and a sequence-annealing alignment,
       instead of the traditional progressive alignment method. It is the only
       alignment program that allows to control the sensitivity / specificity
       tradeoff. It is based on the ProbCons source code, but uses alignment
       metric accuracy and eliminates the consistency transformation.

       In its default configuration, AMAP is tuned to maximize the expected
       Alignment Metric Accuracy (AMA) score - a new alignment accuracy
       measure, based on a metric for the multiple-alignment space, which
       integrates sensitivity and specificity into a single balanced measure.
       AMA is defined as the fraction of correctly aligned residues (either to
       another residue or to a gap) out of the total number of residues in all
       the sequences.

       amap aligns sequences provided in MFA format. This format consists of
       multiple sequences. Each sequence in MFA format begins with a
       single-line description, followed by lines of sequence data. The
       description line is distinguished from the sequence data by a
       greater-than (“>”) symbol in the first column.


           use CLUSTALW output format instead of MFA

       -c --consistency REPS
           use 0 <= REPS <= 5 (default: 0) passes of consistency

       -ir --iterative-refinement REPS
           use 0 <= REPS <=1000 (default: 0) passes of iterative-refinement

       -pre --pre-training REPS
           use 0 <= REPS <= 20 (default: 0) rounds of pretraining

           generate all-pairs pairwise alignments

           use Viterbi algorithm to generate all pairs (automatically enables

       -v --verbose
           Report progress while aligning (default: off)

       -annot FILENAME
           write annotation for multiple alignment to FILENAME

       -t --train FILENAME
           compute EM transition probabilities, store in FILENAME (default: no

       -e --emissions
           also reestimate emission probabilities (default: off)

       -p --paramfile FILENAME
           read parameters from FILENAME (default: )

       -a --alignment-order
           print sequences in alignment order rather than input order
           (default: off)

       -g --gap-factor GF
           use GF as the gap-factor parameter, set to 0 for best sensitivity,
           higher values for better specificity (default: 0.5)

       -w --edge-weight-threshold W
           stop the sequence annealing process when best edge has lower weight
           than W, set to 0 for best sensitivity, higher values for better
           specificity (default: 0)

       -prog --progressive
           use progressive alignment instead of sequence annealing alignment
           (default: off)

       -noreorder --no-edge-reordering
           disable reordering of edges during sequence annealing alignment
           (default: off)

       -maxstep --use-max-stepsize
           use maximum improvement step size instead of tGf edge ranking
           (default: off)

       -print --print-posteriors
           only print the posterior probability matrices (default: off)

       -gui START STEP
           print output for the AMAP Display Java based GUI (default: )
           starting at weight START (default: infinity) with step size STEP
           (default: )


       To run AMAP with the default options change to the align directory and

       % amap <multi-fasta-file-name>

       If no file name is provided the list of options are printed.

       In order to use the AMAP Display run AMAP with the -gui option, and
       save the output to a file, then use the file as the input to
       AmapDisplay. For example, type:

       % align/amap -gui examples/BB12020.tfa > examples/BB12020.tfa.out

       % java -jar display/AmapDisplay.jar examples/BB12020.tfa.out

       (on Debian systems, the examples directory is in


       In older versions ( < 2.0-1) of the package for Debian(TM) systems, the
       amap command was renamed amap-align because there was already another
       tool called amap (which performs some computer network diagnostics). A
       symbolic link amap-align is still provided for upgrade purposes but
       will be removed in Debian releases posterior to Etch (Debian 4.0).


       The current version of AMAP uses the PROBCONS 1.09 code base for some
       of the input/output procedures, and for the calculation of posterior
       probabilities (see PROBCONS.README in /usr/share/doc/amap-align/).
       Future releases might implement the algorithm using a new independent
       code base.

       On Debian(TM) systems, probcons(1) is available in the probcons


       For more details on AMAP and AMA, see Schwartz, Ariel S., Myers, Eugene
       W., and Pachter, Lior. Alignment Metric Accuracy (Submitted for
       publication). For more details on sequence-annealing, see Schwartz,
       Ariel S. and Pachter, Lior. Multiple Alignment by Sequence Annealing
       (Submitted for publication).

       PROBCONS was published in Do, C.B., Mahabhashyam, M.S.P., Brudno, M.,
       and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based
       Multiple Sequence Alignment. Genome Research 15: 330-340.


       Ariel Schwartz <>
           Upstream author of AMAP

       Chuong Do
           Wrote Probcons, on which AMAP is based.

       Charles Plessy> <>
           Wrote this manpage in DocBook XML for the Debian distribution.


       AMAP, PROBCONS, and this manual page have been made freely available as
       PUBLIC DOMAIN software and hence are not subject to copyright in the
       United States. This system and/or any portion of the source code may be
       used, modified, or redistributed without restrictions. AMAP, PROBCONS
       and this manual page are distributed WITHOUT WARRANTY, express or
       implied. The authors accept NO LEGAL LIABILITY OR RESPONSIBILITY for
       loss due to reliance on the program.