--- /dev/null
+.TH ANALYSESEQS l
+.ER
+.SH NAME
+AnalyseSeqs \- Analyse a set of sequences of common length
+.SH SYNOPSIS
+\fBAnalyseSeqs [\-X[\fIbswn\fP]] [\-Q] [\-M{mask}[+|!]] [\-D{H|A|G}] [\-d{S|H|D|B}]
+.SH DESCRIPTION
+.I AnalyseSeqs
+reads a set of sequences from stdin and tries a variety of methods
+for sequence analysis on them. Currently available are:
+.br
+Statistical geometry for quadruples of sequences; THIS IS
+PRELIMINARY AND NOT WELL TESTED BY NOW.
+.br
+split decomposition;
+neighbour joining and Ward's variance method for reconstructing
+phylogenies using various distance measures.
+For statistical geometry and the cluster methods PostScript output
+is available.
+.br
+The program continues reading until it encounters one of the
+separator characters '@' or '%'. Only sequences of alphabetical
+characters or of a specified alphabet are processed, all other
+lines are ignored. The program stops reading
+if it either encounters an EOF condition, or if there are no
+valid sequence data between two lines beginning with separator
+characters.
+.br
+A list of taxa names can be specified in the input stream. The list
+begins with a line beginning with '*'. Optionally, a file name prefix
+[fn] for the PostScript output can be specified in this line.
+The entries have the form 'x : Taxon',
+where x is the number of taxon, i.e., of the corresponding entry in
+the list of input sequences. The taxa list need not be complete. It must
+end, however, with a line beginning with '*' or any of the separator
+characters. The taxa list is printed on top of the output. The specified
+taxa names are used as labels in the PostScript output.
+
+.SH OPTIONS
+.IP \fB\-X[bswn]\fI\fP
+specifies the analysis methods to be used.
+.IP \fB[b]\fI\fP
+Statistical Geometry. A PostScript file named '[fn_]box.ps' giving a
+graphical representation of the statistical geometry is created. The
+resulting box is a good measure of 'tree likeness' of the data set.
+This is the default.
+.IP \fB[s]\fI\fP
+Split decomposition.
+.IP \fB[w]\fI\fP
+Cluster analysis using Ward's method. A PostScript file named '[fn_]wards.ps'
+is created containing a drawing of the tree.
+.IP \fB[n]\fI\fP
+Cluster analysis using Saitou's neighbour joining method. A PostScript
+file named '[fn_]nj.ps' is created containing a drawing of the tree.
+
+.IP \fB\-Q\fB
+indicates that a statistical geometry analysis is to be performed
+comparing four data sets, for instance to confirm the significance of
+a proposed phylogeny. This option is only useful for statistical
+geometry analysis and hence the -X option is ignored. Each of the
+four data sets must be of the form
+.br
+* [filename_prefix]
+.br
+# number
+.br
+[list of taxa names]
+.br
+*
+.br
+list of sequences
+.br
+%
+.br
+where number is 1,2,3,4 for the four groups to be compared.
+
+.IP \fB\-M{mask}[+|!]\fB
+allows to specify a mask for the input file. '{mask}' can be one
+of the following letters indicating a predefined alphabet or
+the %-sign followed by all characters to be accepted. A + sign
+at the very end of the mask indicates that the input is to be
+handled case sensitive. Default is conversion of the input to
+upper case. A ! sign can be used to convert the input data to
+RY code: GgAaXx -> R, UuCcKkTt -> Y, all other letters are
+converted to *.
+.IP \fB-Ma\fI\fP
+all letters A-Z and a-z.
+.IP \fB-Mu\fI\fP
+uppercase letters.
+.IP \fB-Ml\fI\fP
+lowercase letters.
+.IP \fB-Mc\fI\fP
+digits [0-9].
+.IP \fB-Mn\fI\fP
+all alphanumeric characters.
+.IP \fB-MR\fI\fP
+RNA alphabet (GCAUgcau).
+.IP \fB-MD\fI\fP
+DNA alphabet (GCATgcat).
+.IP \fB-MA\fI\fP
+Amino acids in one-letter code.
+.IP \fB-MS\fI\fP
+Secondary strcutures coded as '^.()'
+.IP \fB-M%alphabet\fI\fP
+use the specified alphabet.
+
+.IP \fB\-D\fB
+specifies the algorithm to be used for calculating the
+distance matrix of the input data set. Available are
+.IP \fB-DH\fI\fP
+Hamming Distance
+.IP \fB-DA[,cost]\fI\fB
+Simple alignment distance according to Needleman and Wunsch.
+A gap cost different from 1. can be specified after the comma.
+.IP \fB-DG[,cost1,cost2]\fI\fB
+Gotoh's distance with gap cost function
+g(k) = cost2+cost1*(k-1). cost2<=cost1 has to be fulfilled.
+Default values are cost1=1., cost2=1., yielding the same
+distance as option A.
+.br
+ONLY THE HAMMING DISTANCE IS WELL TESTED BY NOW !!!
+
+.IP \fB\-d\fB
+specifies the edit cost matrix to be used. Available are
+.IP \fB-dS\fI\fP
+simple distance. Indel and substitution of different characters
+all have cost 1. The indel cost can be set by specifying the
+gap costs with the algorithm options -DA and -DG. This is the
+default.
+.IP \fB-dH\fI\fP
+A distance matrix for RNA secondary structures. Inspired by
+Hogeweg's similarity measure (J.Mol.Biol 1988).
+Gap-function is set automatically.
+.IP \fB-dD\fI\fP
+Dayhoff's matrix for amino acid distances.
+.IP \fB-dB\fI\fP
+Distinguish purines and pyrimidines only.
+CAUTION this option of course influences only the calculation of distances.
+It does NOT affect computation of the statistical geometry. This is
+done directly on the sequences. If you want to do statistical geometry on
+RY sequences use the ! sign with the -M option, for instance -MR!.
+
+.SH REFERENCES
+The method of statistical geometry has been introduced by
+M. Eigen, R. Winkler-Oswatitsch and A.W.M. Dress
+(Proc Natl Acad Sci, 85:1988,5912).
+The method of split decomposition was proposed by
+H.J. Bandelt and A.W.M. Dress
+(Adv Math, 92:1992,47).
+The variance method for cluster analysis is due to H.J. Ward
+(J Amer Stat Ass, 58:1963,236).
+The neighbour joining method was published by Saitou and Nei
+(Mol Biol Evol, 4:1987,406).
+
+This program is part of the Vienna RNA Package
+
+.SH WARNING
+This is the beta test version. Some options or combinations
+of options may still produce nonsense. Please send bug reports to
+ivo@tbi.univie.ac.at.
+
+.SH VERSION
+This man page is part of the Vienna RNA Package version 1.2.
+.SH AUTHOR
+Peter F Stadler, Ivo L. Hofacker.
+.SH BUGS
+Comments should be sent to ivo@itc.univie.ac.at.
+.br
git://source.jalview.org / jabaws.git / blobdiff