{"type":"doc","content":[{"type":"extension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"include","parameters":{"macroParams":{"":{"value":"docs:_DE_archived_apps_blurb"}},"macroMetadata":{"schemaVersion":{"value":"1"},"title":"Include Page"}}}},{"type":"heading","attrs":{"level":2},"content":[{"text":" ","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]},{"text":"This Application has been archived. Please see the new RAxML 8.1.17 app.","type":"text","marks":[{"type":"textColor","attrs":{"color":"#ff0000"}},{"type":"strong"}]},{"text":" ","type":"text","marks":[{"type":"textColor","attrs":{"color":"#800080"}}]}]},{"type":"paragraph","content":[{"text":" ","type":"text","marks":[{"type":"textColor","attrs":{"color":"#000000"}}]},{"type":"inlineExtension","attrs":{"extensionType":"com.atlassian.confluence.migration","extensionKey":"__confluenceADFMigrationUnsupportedContentInternalExtension__","text":"","parameters":{"cxhtml":"INLINEStaff

GainsboroOrangeVISIBLE ONLY TO STAFF - CONTENT HIDDEN FOR DEPRECATED APP

App Name

RAxML implements a rapid maximum likelihood-based inference of large phylogenetic trees from amino acid multiple sequence alignments.

Quick Start

To use RAxML, upload your data in relaxed PHYLIP format (sequential or interleaved, no name length restrictions).
Resources: documentation

Test Data

All files are located in the Community Data directory of the iPlant Discovery Environment at the following path:

Community Data > iplantcollaborative > example_data > raxml_proteins

Input File(s)

Use muscle.alignment.interleaved.phylip as test data.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

Model: PROTAT, Substitution Matrix BLOSUM62.

Output File(s)

Expect as output:

: best Rapid ML tree
: run info
: run log
: parsimony-generated base tree
: result tree

Please note that due to the randomization of the algorithm, your outputs may not be EXACTLY the same as those listed in the example data directory.

Tool Source

http://wwwkramer.in.tum.de/exelixis/software.html

","nestedContent":{"type":"doc","content":[{"type":"bodiedExtension","attrs":{"extensionType":"com.atlassian.confluence.macro.core","extensionKey":"show-if","parameters":{"macroParams":{"atlassian-macro-output-type":{"value":"INLINE"},"group":{"value":"Staff"}},"macroMetadata":{"schemaVersion":{"value":"1"},"title":"show-if"}}},"content":[{"type":"table","attrs":{"layout":"default"},"content":[{"type":"tableRow","content":[{"type":"tableHeader","attrs":{"colspan":1,"background":"Orange","rowspan":1},"content":[{"type":"paragraph","content":[{"text":"VISIBLE ONLY TO STAFF - CONTENT HIDDEN FOR DEPRECATED APP","type":"text","marks":[{"type":"strong"}]}]}]}]},{"type":"tableRow","content":[{"type":"tableCell","attrs":{"colspan":1,"background":"Gainsboro","rowspan":1},"content":[{"type":"heading","attrs":{"level":1},"content":[{"text":"App Name","type":"text"}]},{"type":"paragraph","content":[{"text":"RAxML","type":"text","marks":[{"type":"link","attrs":{"href":"http://wwwkramer.in.tum.de/exelixis/software.html"}},{"type":"strong"}]},{"text":" implements a rapid maximum likelihood-based inference of large phylogenetic trees from amino acid multiple sequence alignments.","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Quick Start","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"To use RAxML,","type":"text","marks":[{"type":"strong"}]},{"text":" upload your data in relaxed PHYLIP format (sequential or interleaved, no name length restrictions).","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Resources:","type":"text","marks":[{"type":"strong"}]},{"text":" ","type":"text"},{"text":"documentation","type":"text","marks":[{"type":"link","attrs":{"href":"http://wwwkramer.in.tum.de/exelixis/software.html"}}]}]}]}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Test Data","type":"text"}]},{"type":"heading","attrs":{"level":5},"content":[{"text":"All files are located in the Community Data directory of the iPlant Discovery Environment at the following path:","type":"text"}]},{"type":"paragraph","content":[{"text":"Community Data > iplantcollaborative > example_data > raxml_proteins","type":"text","marks":[{"type":"em"},{"type":"strong"}]}]},{"type":"heading","attrs":{"level":4},"content":[{"text":"Input File(s)","type":"text"}]},{"type":"paragraph","content":[{"text":"Use muscle.alignment.interleaved.phylip as test data.","type":"text"}]},{"type":"heading","attrs":{"level":4},"content":[{"text":"Parameters Used in App","type":"text"}]},{"type":"paragraph","content":[{"text":"When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Model: PROTAT, Substitution Matrix BLOSUM62.","type":"text"}]}]}]},{"type":"heading","attrs":{"level":4},"content":[{"text":"Output File(s)","type":"text"}]},{"type":"paragraph","content":[{"text":"Expect as output:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"RAxML_bestTree.tree.nwk","type":"text","marks":[{"type":"link","attrs":{"href":"https://cyverse.atlassian.net/wiki/download/attachments/241882186/RAxML_bestTree.tree.nwk?version=1&modificationDate=1323798522000&cacheVersion=1&api=v2"}}]},{"text":": best Rapid ML tree","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"RAxML_info.tree.nwk","type":"text","marks":[{"type":"link","attrs":{"href":"https://cyverse.atlassian.net/wiki/download/attachments/241882186/RAxML_info.tree.nwk?version=1&modificationDate=1323798523000&cacheVersion=1&api=v2"}}]},{"text":": run info","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"RAxML_log.tree.nwk","type":"text","marks":[{"type":"link","attrs":{"href":"https://cyverse.atlassian.net/wiki/download/attachments/241882186/RAxML_log.tree.nwk?version=1&modificationDate=1323798523000&cacheVersion=1&api=v2"}}]},{"text":": run log","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"RAxML_parsimonyTree.tree.nwk","type":"text","marks":[{"type":"link","attrs":{"href":"https://cyverse.atlassian.net/wiki/download/attachments/241882186/RAxML_parsimonyTree.tree.nwk?version=1&modificationDate=1323798523000&cacheVersion=1&api=v2"}}]},{"text":": parsimony-generated base tree","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"RAxML_result.tree.nwk","type":"text","marks":[{"type":"link","attrs":{"href":"https://cyverse.atlassian.net/wiki/download/attachments/241882186/RAxML_result.tree.nwk?version=1&modificationDate=1323798523000&cacheVersion=1&api=v2"}}]},{"text":": result tree","type":"text"}]}]}]},{"type":"paragraph","content":[{"text":"Please note that due to the randomization of the algorithm, your outputs may not be EXACTLY the same as those listed in the example data directory.","type":"text","marks":[{"type":"strong"}]}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Tool Source","type":"text"}]},{"type":"paragraph","content":[{"text":"http://wwwkramer.in.tum.de/exelixis/software.html","type":"text","marks":[{"type":"link","attrs":{"href":"http://wwwkramer.in.tum.de/exelixis/software.html"}}]}]}]}]}]}]}],"version":1}}}},{"type":"hardBreak"}]}],"version":1}

RAxML - Proteins (archived)

This Application has been archived. Please see the new RAxML 8.1.17 app.