4 AnalyseSeqs \- Analyse a set of sequences of common length
6 \fBAnalyseSeqs [\-X[\fIbswn\fP]] [\-Q] [\-M{mask}[+|!]] [\-D{H|A|G}] [\-d{S|H|D|B}]
9 reads a set of sequences from stdin and tries a variety of methods
10 for sequence analysis on them. Currently available are:
12 Statistical geometry for quadruples of sequences; THIS IS
13 PRELIMINARY AND NOT WELL TESTED BY NOW.
16 neighbour joining and Ward's variance method for reconstructing
17 phylogenies using various distance measures.
18 For statistical geometry and the cluster methods PostScript output
21 The program continues reading until it encounters one of the
22 separator characters '@' or '%'. Only sequences of alphabetical
23 characters or of a specified alphabet are processed, all other
24 lines are ignored. The program stops reading
25 if it either encounters an EOF condition, or if there are no
26 valid sequence data between two lines beginning with separator
29 A list of taxa names can be specified in the input stream. The list
30 begins with a line beginning with '*'. Optionally, a file name prefix
31 [fn] for the PostScript output can be specified in this line.
32 The entries have the form 'x : Taxon',
33 where x is the number of taxon, i.e., of the corresponding entry in
34 the list of input sequences. The taxa list need not be complete. It must
35 end, however, with a line beginning with '*' or any of the separator
36 characters. The taxa list is printed on top of the output. The specified
37 taxa names are used as labels in the PostScript output.
40 .IP \fB\-X[bswn]\fI\fP
41 specifies the analysis methods to be used.
43 Statistical Geometry. A PostScript file named '[fn_]box.ps' giving a
44 graphical representation of the statistical geometry is created. The
45 resulting box is a good measure of 'tree likeness' of the data set.
50 Cluster analysis using Ward's method. A PostScript file named '[fn_]wards.ps'
51 is created containing a drawing of the tree.
53 Cluster analysis using Saitou's neighbour joining method. A PostScript
54 file named '[fn_]nj.ps' is created containing a drawing of the tree.
57 indicates that a statistical geometry analysis is to be performed
58 comparing four data sets, for instance to confirm the significance of
59 a proposed phylogeny. This option is only useful for statistical
60 geometry analysis and hence the -X option is ignored. Each of the
61 four data sets must be of the form
75 where number is 1,2,3,4 for the four groups to be compared.
77 .IP \fB\-M{mask}[+|!]\fB
78 allows to specify a mask for the input file. '{mask}' can be one
79 of the following letters indicating a predefined alphabet or
80 the %-sign followed by all characters to be accepted. A + sign
81 at the very end of the mask indicates that the input is to be
82 handled case sensitive. Default is conversion of the input to
83 upper case. A ! sign can be used to convert the input data to
84 RY code: GgAaXx -> R, UuCcKkTt -> Y, all other letters are
87 all letters A-Z and a-z.
95 all alphanumeric characters.
97 RNA alphabet (GCAUgcau).
99 DNA alphabet (GCATgcat).
101 Amino acids in one-letter code.
103 Secondary strcutures coded as '^.()'
104 .IP \fB-M%alphabet\fI\fP
105 use the specified alphabet.
108 specifies the algorithm to be used for calculating the
109 distance matrix of the input data set. Available are
112 .IP \fB-DA[,cost]\fI\fB
113 Simple alignment distance according to Needleman and Wunsch.
114 A gap cost different from 1. can be specified after the comma.
115 .IP \fB-DG[,cost1,cost2]\fI\fB
116 Gotoh's distance with gap cost function
117 g(k) = cost2+cost1*(k-1). cost2<=cost1 has to be fulfilled.
118 Default values are cost1=1., cost2=1., yielding the same
119 distance as option A.
121 ONLY THE HAMMING DISTANCE IS WELL TESTED BY NOW !!!
124 specifies the edit cost matrix to be used. Available are
126 simple distance. Indel and substitution of different characters
127 all have cost 1. The indel cost can be set by specifying the
128 gap costs with the algorithm options -DA and -DG. This is the
131 A distance matrix for RNA secondary structures. Inspired by
132 Hogeweg's similarity measure (J.Mol.Biol 1988).
133 Gap-function is set automatically.
135 Dayhoff's matrix for amino acid distances.
137 Distinguish purines and pyrimidines only.
138 CAUTION this option of course influences only the calculation of distances.
139 It does NOT affect computation of the statistical geometry. This is
140 done directly on the sequences. If you want to do statistical geometry on
141 RY sequences use the ! sign with the -M option, for instance -MR!.
144 The method of statistical geometry has been introduced by
145 M. Eigen, R. Winkler-Oswatitsch and A.W.M. Dress
146 (Proc Natl Acad Sci, 85:1988,5912).
147 The method of split decomposition was proposed by
148 H.J. Bandelt and A.W.M. Dress
149 (Adv Math, 92:1992,47).
150 The variance method for cluster analysis is due to H.J. Ward
151 (J Amer Stat Ass, 58:1963,236).
152 The neighbour joining method was published by Saitou and Nei
153 (Mol Biol Evol, 4:1987,406).
155 This program is part of the Vienna RNA Package
158 This is the beta test version. Some options or combinations
159 of options may still produce nonsense. Please send bug reports to
160 ivo@tbi.univie.ac.at.
163 This man page is part of the Vienna RNA Package version 1.2.
165 Peter F Stadler, Ivo L. Hofacker.
167 Comments should be sent to ivo@itc.univie.ac.at.
git://source.jalview.org / jabaws.git / blob