+
+AA Conservation version 1.0b (2 September 2010)
+
+This program allows calculation of conservation of amino acids in
+multiple sequence alignments.
+It implements 17 different conservation scores as described by Valdar in
+his paper (Scoring Residue Conservation, PROTEINS: Structure, Function
+and Bioinformatics 48:227-241 (2002)) and SMERFS scoring algorithm as described
+by Manning, Jefferson and Barton (The contrasting properties of conservation
+and correlated phylogeny in protein functional residue prediction,
+BMC Bioinformatics (2008)).
+
+The conservation algorithms supported are:
+
+KABAT, JORES, SCHNEIDER, SHENKIN, GERSTEIN, TAYLOR_GAPS, TAYLOR_NO_GAPS,
+ZVELIBIL, KARLIN, ARMON, THOMPSON, NOT_LANCET, MIRNY, WILLIAMSON,
+LANDGRAF, SANDER, VALDAR, SMERFS
+
+Input format is either a FASTA formatted file containing aligned sequences with
+gaps or a Clustal alignment. The valid gap characters are *, -, space character,
+X and . (a dot). By default program prints the results to the command window.
+If the output file is provided the results are printed to the file in two
+possible formats with or without an alignment.
+If format is not specified, the program outputs conservation scores without
+alignment. The scores are not normalized by default but they can be (see below).
+SMERFS default parameters are window width of 7, column score is set to
+the middle column (MID_SCORE), gap% cutoff of 0.1. Different parameters for SMERFS
+can be provided (see below). Details of the program execution can be recorded to
+a separate file if an appropriate file path is provided.
+
+List of command line arguments:
+
+-m= precedes a comma separated list of method names
+ EXAMPLE: -m=KABAT,JORES,GERSTEIN
+ Optional, if no method is specified request for all is assumed.
+
+-i= precedes a full path to the input FASTA file, required
+
+-o= precedes a full path to the output file, optional, if no output file is
+ provided the program will output to the standard out.
+
+-t= precedes the number of CPUs (CPU cores more precisely) to use. Optional,
+ defaults to all processors available on the machine.
+
+-f= precedes the format of the results in the output file
+ two different formats are possible:
+ RESULT_WITH_ALIGNMENT
+ RESULT_NO_ALIGNMENT
+ Optional, if not specified RESULT_NO_ALIGNMENT is assumed
+
+-d= precedes a full path to a file where program execution details are to be
+ listed. Optional, if not provided, no execution statistics is produced.
+
+-g= precedes comma separated list of gap characters provided by the user, if
+ you're using an unusual gap character (not a -,., ,*,X) you have to
+ provide it. If you you provide this list you have to list all the gaps
+ accepted. Including those that were previously treated as a default.
+ Optional.
+
+-n using this key causes the results to be normalized.
+ Normalized results have values between 0 and 1. Please note however, that
+ some results cannot be normalized. In such a case, the system returns not
+ normalized value, and log the issue to the standard error stream.
+ The following formula is used for normalization
+ n = (d - dmin)/(dmax - dmin)
+ Negative results first converted to positive by adding an absolute value of
+ the most negative result. Optional.
+
+SMERFS Only Parameters:
+
+-smerfsGT= precedes SMERFS Gap Treshold - a gap percentage cutoff -
+ a float greater than 0 and smaller or equal 1. Optional defaults
+ to 0.1
+
+-smerfsCS= precedes SMERFS Column Score algorithm defines the window scores to
+ columns allocation , two methods are possible:
+ MID_SCORE - gives the window score to the middle column
+ MAX_SCORE - gives the column the highest score of all the windows it
+ belongs to. Optional defaults to MID_SCORE.
+
+-smerfsWW= precedes Window Width parameter - an integer and an odd number.
+ Optional, defaults to 7
+
+
+EXAMPLE HOW TO RUN THE PROGRAM:
+java -jar <jar name> -m=KABAT,SMERFS -i=prot1 -o=prot1_results -n
+
+As a result of the execution KABAT and SMERFS scores will be calculated.
+Input comes form prot1 file and an output without an alignment is recorded to
+prot1_results file.
+
+Authors: Peter Troshin, Agnieszka Golicz, David Martin and Geoff Barton.
+Please visit http://www.compbio.dundee.ac.uk/aacon for further information.
+
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