├── .travis.yml ├── INSTALL.pl ├── ProphET_standalone.pl ├── README.md ├── README_BROAD_USERS.md ├── README_INSTALLING_PERL_MODULES.md ├── UTILS.dir ├── extrair_ncbi_prophage_families.pl ├── fasta2line ├── fetch_genomes_based_on_taxid.pl ├── gff2gene_protein_seq.pl ├── gff2graph-from-scratch.pl ├── line2fasta ├── obtain_prot_with_annot_seq.pl ├── retrieve_proteins.SLOW.sh ├── retrieve_proteins.sh ├── script_remover_vazios.pl ├── split_genbank.pl ├── splitfasta.pl └── union.pl ├── config.dir ├── ABC_transporters_to_grep.txt ├── Prophages_names_sem_Claviviridae_Guttaviridae-TxID └── Prophages_names_sem_Claviviridae_Guttaviridae-TxID.SMOKE_TEST ├── expected_output_of_test ├── NC_005362.1.phage_1.fas ├── NC_005362.1.phage_2.fas └── phages_coords ├── test.fasta └── test.gff /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jaumlrc/ProphET/HEAD/.travis.yml 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