passes of consistency transformation\r
</description>\r
<optionNames>-c</optionNames>\r
- <optionNames>--consistency</optionNames>\r
<furtherDetails>prog_docs/msaprobs.txt</furtherDetails>\r
<defaultValue>2</defaultValue>\r
<validValue>\r
number of passes of iterative-refinement\r
</description>\r
<optionNames>-ir</optionNames>\r
- <optionNames>--iterative-refinement</optionNames>\r
<furtherDetails>prog_docs/msaprobs.txt</furtherDetails>\r
<defaultValue>10</defaultValue>\r
<validValue>\r