NAME

       amap - Protein multiple alignment by sequence annealing

SYNOPSIS

       amap [OPTION] [MFAFILE] [MFAFILE]

DESCRIPTION

       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 one 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.

OPTIONS

       -clustalw
           use CLUSTALW output format instead of MFA

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

       -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

       -pairs
           generate all-pairs pairwise alignments

       -viterbi
           use Viterbi algorithm to generate all pairs (automatically enables -pairs)

       -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 training)

       -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: )

EXAMPLES

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

       % 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 /usr/share/doc/amap-align/examples

NOTE

       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).

SEE ALSO

       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 package.

REFERENCES

       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.

AUTHORS

       Ariel Schwartz <sariel@cs.berkeley.edu>
           Upstream author of AMAP

       Chuong Do
           Wrote Probcons, on which AMAP is based.

       Charles Plessy> <charles-debian-nospam@plessy.org>
           Wrote this manpage in DocBook XML for the Debian distribution.

COPYRIGHT

       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.