Workflow Type: Galaxy
Frozen
Phylogenetic reconstruction using genome-wide and single-gene alignment data. Here we use maximum likelihood reconstruction program IQTree. Data can be prepared using the phylogenetic data preparation workflow prior to phylogenetic reconstruction. Resulting trees can be viewed interactively using Galaxy's 'Phyloviz' or 'Phylogenetic Tree Visualization'
Inputs
ID | Name | Description | Type |
---|---|---|---|
Input alignment collection | Input alignment collection | n/a |
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Steps
ID | Name | Description |
---|---|---|
1 | IQ-TREE | toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/1.5.5.3 |
2 | ClipKIT. Alignment trimming software for phylogenetics. | toolshed.g2.bx.psu.edu/repos/padge/clipkit/clipkit/0.1.0 |
3 | ASTRAL-III. Tool for estimating an unrooted species tree given a set of unrooted gene trees. | toolshed.g2.bx.psu.edu/repos/padge/astral/astral/0.1.0 |
4 | PhyKit - Alignment-based functions | toolshed.g2.bx.psu.edu/repos/padge/phykit/phykit_alignment_based/0.1.0 |
5 | IQ-TREE | toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/1.5.5.3 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
_anonymous_output_1 | _anonymous_output_1 | n/a |
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_anonymous_output_2 | _anonymous_output_2 | n/a |
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_anonymous_output_3 | _anonymous_output_3 | n/a |
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_anonymous_output_4 | _anonymous_output_4 | n/a |
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_anonymous_output_5 | _anonymous_output_5 | n/a |
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_anonymous_output_6 | _anonymous_output_6 | n/a |
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Trimmed alignment. | Trimmed alignment. | n/a |
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Output tree file | Output tree file | n/a |
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Astral log. | Astral log. | n/a |
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An occupancy file that summarizes the taxon occupancy per sequence | An occupancy file that summarizes the taxon occupancy per sequence | n/a |
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Concatenated fasta alignment file | Concatenated fasta alignment file | n/a |
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A partition file ready for input into RAxML or IQ-tree | A partition file ready for input into RAxML or IQ-tree | n/a |
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IQ-TREE on input dataset(s): BIONJ Tree | IQ-TREE on input dataset(s): BIONJ Tree | n/a |
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IQ-TREE on input dataset(s): MaxLikelihood Tree | IQ-TREE on input dataset(s): MaxLikelihood Tree | n/a |
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IQ-TREE on input dataset(s): Consensus Tree | IQ-TREE on input dataset(s): Consensus Tree | n/a |
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IQ-TREE on input dataset(s): MaxLikelihood Distance Matrix | IQ-TREE on input dataset(s): MaxLikelihood Distance Matrix | n/a |
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IQ-TREE on input dataset(s): Report and Final Tree | IQ-TREE on input dataset(s): Report and Final Tree | n/a |
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IQ-TREE on input dataset(s): Occurence Frequencies in Bootstrap Trees | IQ-TREE on input dataset(s): Occurence Frequencies in Bootstrap Trees | n/a |
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Version History
Version 1 (earliest) Created 6th Jun 2022 at 15:14 by Miguel Roncoroni
Initial commit
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Version-1
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Creators and Submitter
Creators
Not specifiedAdditional credit
Miguel Roncoroni
Submitter
Tool
Activity
Views: 3201 Downloads: 210 Runs: 3
Created: 6th Jun 2022 at 15:14
Attributions
None