{"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":"paragraph","content":[{"text":" ","type":"text"}]},{"type":"paragraph","content":[{"text":" ","type":"text"},{"type":"inlineExtension","attrs":{"extensionType":"com.atlassian.confluence.migration","extensionKey":"__confluenceADFMigrationUnsupportedContentInternalExtension__","text":"","parameters":{"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":"Phylogenetics Muscle-PhyML","type":"text"}]},{"type":"paragraph","content":[{"text":"Simple phylogenetics using Muscle for multiple sequence alignment and PhyML for phylogenetic tree reconstruction.","type":"text"}]},{"type":"paragraph","content":[{"text":"Quick Start","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Specify a fasta file for the analysis","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Make sure the sequence type (amino acid or dna) is set correctly","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Have fun!","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Note: you may visualize the tree using iPlant's build in Tree Viewer","type":"text"}]}]}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Test Data","type":"text"}]},{"type":"panel","attrs":{"panelType":"info"},"content":[{"type":"paragraph","content":[{"text":"Test data for this app appears directly in the Discovery Environment in the Data window under ","type":"text"},{"text":"Community Data -> iplantcollaborative -> example_data ->","type":"text","marks":[{"type":"em"}]},{"text":" ","type":"text"},{"text":"muscle_named_outputs","type":"text","marks":[{"type":"em"}]},{"text":".","type":"text"}]},{"type":"paragraph","content":[{"text":"Note, this workflow using the same test input data as that for \"Muscle named outputs\" as that integration of Muscle is the first tool of this workflow.","type":"text"}]}]},{"type":"heading","attrs":{"level":4},"content":[{"text":"Input File(s)","type":"text"}]},{"type":"paragraph","content":[{"text":"Fasta sequence file","type":"text"}]},{"type":"paragraph","content":[{"text":"Note: The sequence names cannot have any spaces in them as that causes problems with PhyML. Also, the first 15 characters of the name should be unique.","type":"text"}]},{"type":"heading","attrs":{"level":4},"content":[{"text":"Parameters Used in App","type":"text"}]},{"type":"paragraph","content":[{"text":"Specifying if the sequence is amino acid or dna. This is set for each of the two tools in the workflow, Muscle and PhyML. ","type":"text"}]},{"type":"paragraph","content":[{"text":"Default:","type":"text"}]},{"type":"bulletList","content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Muscle: automatic detection of sequence type","type":"text"}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"PhyML: Amino Acid","type":"text"}]}]}]},{"type":"heading","attrs":{"level":4},"content":[{"text":"Output File(s)","type":"text"}]}]}]}]}]}],"version":1},"cxhtml":"INLINEStaff

GainsboroOrangeVISIBLE ONLY TO STAFF - CONTENT HIDDEN FOR DEPRECATED APP

Phylogenetics Muscle-PhyML

Simple phylogenetics using Muscle for multiple sequence alignment and PhyML for phylogenetic tree reconstruction.

Quick Start

Specify a fasta file for the analysis
Make sure the sequence type (amino acid or dna) is set correctly
Have fun!
Note: you may visualize the tree using iPlant's build in Tree Viewer

Test Data

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> muscle_named_outputs.

Note, this workflow using the same test input data as that for "Muscle named outputs" as that integration of Muscle is the first tool of this workflow.

Input File(s)

Fasta sequence file

Note: The sequence names cannot have any spaces in them as that causes problems with PhyML. Also, the first 15 characters of the name should be unique.

Parameters Used in App

Specifying if the sequence is amino acid or dna. This is set for each of the two tools in the workflow, Muscle and PhyML.

Default:

Muscle: automatic detection of sequence type
PhyML: Amino Acid

Output File(s)

"}}}]}],"version":1}

Phylogenetics Muscle-PhyML (archived)