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amap - Protein multiple alignment by sequence annealing




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.


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

generate all-pairs pairwise alignments

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

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

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)

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 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


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).

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