Table 1:
Galaxy tools used in the workflow
| Developed at Earlham Institute | Toolsheds | ||||
|---|---|---|---|---|---|
| Tool name | Tool ID | Version | Tool | Wrapper | reference |
| Get sequences by Ensembl ID | get_sequences | 0.1.2 | Yes | Yes | [17] |
| Get features by Ensembl ID | get_feature_info | 0.1.2 | Yes | Yes | [18] |
| Select longest coding sequence per gene | ensembl_longest_cds_per_gene | 0.0.2 | Yes | Yes | [19] |
| ETE species tree generator | ete_species_tree_generator | 3.0.0b35 | Yes | Yes | [20] |
| GeneSeqToFamily preparation | gstf_preparation | 0.4.0 | Yes | Yes | [21] |
| Transeq | EMBOSS: transeq101 | 5.0.0 | No | No | [22] |
| NCBI BLAST+ makeblastdb | ncbi_makeblastdb | 0.2.01 | No | No | [23] |
| NCBI BLAST+ blastp | ncbi_blastp_wrapper | 0.2.01 | No | No | [23] |
| BLAST parser | blast_parser | 0.1.2 | Yes | Yes | [24] |
| hcluster_sg | hcluster_sg | 0.5.1.1 | No | Yes | [25] |
| hcluster_sg parser | hcluster_sg_parser | 0.2.0 | Yes | Yes | [26] |
| Filter by FASTA IDs | filter_by_fasta_ids | 1.0 | No | No | [27] |
| T-Coffee | t_coffee | 11.0.8 | No | Yes | [28] |
| Tranalign | EMBOSS: tranalign100 | 5.0.0 | No | No | [22] |
| TreeBeST best | treebest_best | 1.9.2 | No | Yes | [29] |
| Gene Alignment and Family Aggregator | gafa | 0.3.0 | Yes | Yes | [30] |
| Unique | tp_sorted_uniq | 1.1.0 | No | No | [31] |
| FASTA-to-Tabular | fasta2tab | 1.1.0 | No | No | [32] |
| UniProt ID mapping and retrieval | uniprot_rest_interface | 0.1 | No | No | [33] |