1 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
3 <runnerClassName>compbio.runner.structure.RNAalifold</runnerClassName>
4 <options isRequired='false'>
6 <description>Score pairs with endgaps same as gap-gap pairs</description>
7 <optionNames>-E</optionNames>
9 <options isRequired='false'>
10 <name>Most Informative Sequence</name>
11 <description>Ouput Set of nucleotides with frequency > average</description>
12 <optionNames>--mis</optionNames>
14 <options isRequired='false'>
15 <name>Partition Function</name>
16 <description>Output partition function and probability matrix</description>
17 <optionNames>-p</optionNames>
19 <options isRequired='false'>
21 <description>Assume circular RNA molecule</description>
22 <optionNames>-c</optionNames>
24 <!-- Not Currently available with circular structures (-c) -->
25 <options isRequired='false'>
26 <name>G-Quadruplex</name>
27 <description>Incorporate G-Quadruplex formation into prediction algorithm</description>
28 <optionNames>-g</optionNames>
30 <options isRequired='false'>
32 <description>dangling energies will be added for the bases adjacent to a helix on both sides</description>
33 <optionNames>-d2</optionNames>
35 <options isRequired='false'>
37 <description>Produce Structures without lonely pairs</description>
38 <optionNames>--noLP</optionNames>
40 <options isRequired='false'>
42 <description>Do not allow GU pairs</description>
43 <optionNames>--noGU</optionNames>
45 <options isRequired='false'>
46 <name>No Closing GU</name>
47 <description>Do not allow GU pairs at the end of sequences</description>
48 <optionNames>--noClosingGU</optionNames>
50 <options isRequired='false'>
52 <description>Use old energy evaluation, treating gaps as characters</description>
53 <optionNames>--old</optionNames>
55 <options isRequired='false'>
56 <name>Ribosum Scoring</name>
57 <description>Use Ribosum Scoring Matrix</description>
58 <optionNames>-r</optionNames>
60 <options isRequired='false'>
63 Dangling energies are added for the bases adjacent to a helix on both sides
65 <optionNames>-d2</optionNames>
67 <options isRequired='false'>
68 <name>MEA Structure</name>
69 <description>Maximum Expected Accuracy Structure</description>
70 <optionNames>--MEA</optionNames>
73 <prmSeparator> </prmSeparator>
75 <parameters isRequired='false'>
76 <name>scaling factor</name>
77 <description>In calculating pf use scale*mfe as estimate for ensemble free energy]</description>
78 <optionNames>-S</optionNames>
79 <defaultValue>1.07</defaultValue>
86 <parameters isRequired='false'>
87 <name>bppmThreshold</name>
88 <description>Threshold for base pair probabilities</description>
89 <optionNames>--bppmThreshold</optionNames>
90 <defaultValue>0.000001</defaultValue>
97 <parameters isRequired='false'>
98 <name>Temperature</name>
99 <description>Rescale Energy parameterss to Temperature</description>
100 <optionNames>-T</optionNames>
101 <defaultValue>37</defaultValue>
109 <parameters isRequired='false'>
111 <description>weight of covariance term</description>
112 <optionNames>--cfactor</optionNames>
113 <defaultValue>1.0</defaultValue>
120 <parameters isRequired='false'>
122 <description>penalty for non-compatible sequences in covariance term</description>
123 <optionNames>--nfactor</optionNames>
124 <defaultValue>1.0</defaultValue>