preparing genomic data for phylogeny recostruction (GTN) Version 1
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Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Input genomes as collection | #main/Input genomes as collection | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 1 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.2 |
| 2 | RepeatMasker | toolshed.g2.bx.psu.edu/repos/bgruening/repeat_masker/repeatmasker_wrapper/4.1.2-p1+galaxy0 |
| 3 | Funannotate predict annotation | toolshed.g2.bx.psu.edu/repos/iuc/funannotate_predict/funannotate_predict/1.8.9+galaxy2 |
| 4 | Extract ORF | toolshed.g2.bx.psu.edu/repos/bgruening/glimmer_gbk_to_orf/glimmer_gbk_to_orf/3.02 |
| 5 | Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1 |
| 6 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2 |
| 7 | Proteinortho | toolshed.g2.bx.psu.edu/repos/iuc/proteinortho/proteinortho/6.0.14+galaxy2.9.1 |
| 8 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/4.1.4 |
| 9 | Filter | Filter1 |
| 10 | Proteinortho grab proteins | toolshed.g2.bx.psu.edu/repos/iuc/proteinortho_grab_proteins/proteinortho_grab_proteins/6.0.14+galaxy2.9.1 |
| 11 | Regex Find And Replace | toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1 |
| 12 | ClustalW | toolshed.g2.bx.psu.edu/repos/devteam/clustalw/clustalw/2.1 |
| 13 | ClipKIT. Alignment trimming software for phylogenetics. | toolshed.g2.bx.psu.edu/repos/padge/clipkit/clipkit/0.1.0 |
| 14 | PhyKit - Alignment-based functions | toolshed.g2.bx.psu.edu/repos/padge/phykit/phykit_alignment_based/0.1.0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| A partition file ready for input into RAxML or IQ-tree | #main/A partition file ready for input into RAxML or IQ-tree | n/a |
|
| An occupancy file that summarizes the taxon occupancy per sequence | #main/An occupancy file that summarizes the taxon occupancy per sequence | n/a |
|
| ClustalW on input dataset(s): clustal | #main/ClustalW on input dataset(s): clustal | n/a |
|
| Concatenated fasta alignment file | #main/Concatenated fasta alignment file | n/a |
|
| Proteinortho on input dataset(s): orthology-groups | #main/Proteinortho on input dataset(s): orthology-groups | n/a |
|
| Proteinortho_extract_by_orthogroup | #main/Proteinortho_extract_by_orthogroup | n/a |
|
| Trimmed alignment. | #main/Trimmed alignment. | n/a |
|
| _anonymous_output_1 | #main/_anonymous_output_1 | n/a |
|
| _anonymous_output_2 | #main/_anonymous_output_2 | n/a |
|
| _anonymous_output_3 | #main/_anonymous_output_3 | n/a |
|
| _anonymous_output_4 | #main/_anonymous_output_4 | n/a |
|
| _anonymous_output_5 | #main/_anonymous_output_5 | n/a |
|
| _anonymous_output_6 | #main/_anonymous_output_6 | n/a |
|
| _anonymous_output_7 | #main/_anonymous_output_7 | n/a |
|
| extracted_ORFs | #main/extracted_ORFs | n/a |
|
| fasta_header_cleaned | #main/fasta_header_cleaned | n/a |
|
| funannotate_predicted_proteins | #main/funannotate_predicted_proteins | n/a |
|
| headers_shortened | #main/headers_shortened | n/a |
|
| proteomes_to_one_file | #main/proteomes_to_one_file | n/a |
|
| repeat_masked | #main/repeat_masked | n/a |
|
| sample_names_to_headers | #main/sample_names_to_headers | n/a |
|
Version History
2 (earliest) Created 22nd Apr 2024 at 11:11 by Helena Rasche
Added/updated 3 files
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mastered271dc
Creators and Submitter
Views: 40
Created: 22nd Apr 2024 at 11:11
Last updated: 22nd Apr 2024 at 11:11
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