+ <!-- disable as refinew is disabled \r
+ <parameters isRequired="false">\r
+ <name>Maxiters</name>\r
+ <description>Length of window for Window Refine (-refinew)</description>\r
+ <optionNames>-refinewindow</optionNames>\r
+ <furtherDetails>prog_docs/muscle.html</furtherDetails>\r
+ <defaultValue>200</defaultValue>\r
+ <validValue>\r
+ <type>Integer</type>\r
+ <min>1</min>\r
+ <max>1000</max>\r
+ </validValue>\r
+ </parameters>\r
+ -->\r
+ <parameters isRequired="false">\r
+ <name>Diagonal break</name>\r
+ <description>Maximum distance between two diagonals that allows them to merge into one diagonal</description>\r
+ <optionNames>-diagbreak</optionNames>\r
+ <furtherDetails>prog_docs/muscle.html</furtherDetails>\r
+ <defaultValue>1</defaultValue>\r
+ <validValue>\r
+ <type>Integer</type>\r
+ <min>1</min>\r
+ <max>100</max>\r
+ </validValue>\r
+ </parameters>\r
+ <parameters isRequired="false">\r
+ <name>Diagonal length</name>\r
+ <description>Minimum length of diagonal</description>\r
+ <optionNames>-diaglength</optionNames>\r
+ <furtherDetails>prog_docs/muscle.html</furtherDetails>\r
+ <defaultValue>24</defaultValue>\r
+ <validValue>\r
+ <type>Integer</type>\r
+ <min>2</min>\r
+ <max>100</max>\r
+ </validValue>\r
+ </parameters>\r
+ <parameters isRequired="false">\r
+ <name>Diagonal margin</name>\r
+ <description>Discard this many positions at ends of diagonal</description>\r
+ <optionNames>-diagmargin</optionNames>\r
+ <furtherDetails>prog_docs/muscle.html</furtherDetails>\r
+ <defaultValue>5</defaultValue>\r
+ <validValue>\r
+ <type>Integer</type>\r
+ <min>1</min>\r
+ <max>100</max>\r
+ </validValue>\r
+ </parameters>\r
+ <parameters isRequired="false">\r
+ <name>Anchor spacing</name>\r
+ <description>Minimum spacing between anchor columns</description>\r
+ <optionNames>-anchorspacing</optionNames>\r
+ <furtherDetails>prog_docs/muscle.html</furtherDetails>\r
+ <defaultValue>32</defaultValue>\r
+ <validValue>\r
+ <type>Integer</type>\r
+ <min>2</min>\r
+ <max>1000</max>\r
+ </validValue>\r
+ </parameters>\r