├── FRAMA ├── LICENCE.txt ├── README.html ├── README.md ├── example ├── .gitignore ├── paired │ ├── ortholog_cds.fa │ ├── ortholog_table.csv │ ├── reads │ │ ├── reads_R1.fa.gz │ │ └── reads_R2.fa.gz │ ├── reference.gb │ └── testing.cfg └── single │ ├── ortholog_cds.fa │ ├── ortholog_table.csv │ ├── reads │ └── reads.fa.gz │ ├── reference.gb │ └── testing.cfg ├── lib └── perl │ ├── GenbankHelper.pm │ └── StringHelper.pm ├── setup ├── .gitignore ├── SETUP.R ├── SETUP.pl ├── cpanfile ├── programs.yaml └── repeatmasker.cpanfile └── src ├── BBH.pl ├── CDS_predict.pl ├── GO.R ├── KEGG.R ├── Makefile ├── SBH.pl ├── annotation.pl ├── blast_VecScreen.pl ├── blast_filter.pl ├── blast_filterIDs.pl ├── blast_filter_fusion.pl ├── clipping.pl ├── combine_fast.sh ├── contamination_feature.pl ├── fasta_concatenate.pl ├── fasta_mask.pl ├── fasta_unconcat.pl ├── first_occurence.pl ├── genbank2fasta.pl ├── genbank2table.pl ├── genbank_CDS.pl ├── genblasta2table.pl ├── genscan_annotation.pl ├── init.pl ├── parallel_blast.pl ├── parallel_checkLog.R ├── parameter_blast.pl ├── polyamisc ├── README ├── README_training.txt ├── UTR.pl ├── bam_polyA.pl ├── csv_slccontig.pl ├── fasta_trimpolya.pl ├── polyaclip_eval_pipeline.sh ├── polyaclip_eval_scansumcutoff.pl ├── polyaclip_sumscore.pl ├── polyacov_coverage.pl ├── polyacov_dropcov_score.pl ├── polyacov_dropcov_simple.pl ├── polyahomol_score.pl ├── polyaread_score.pl ├── polyas_call_polyar.sh ├── polyaspwm_predict.pl ├── polyaspwm_score.pl ├── polyaspwm_scorenimg.sh ├── polyastrain_call_predict.sh ├── polyastrain_pwm3.pwm └── polyastrain_revscore.pl ├── repCol.pl ├── scaffolding.pl ├── store_hash.pl ├── summarize.R ├── tgicl.pl ├── tgicl.sh ├── trinity_index_reads.pl └── wublast_average.pl /FRAMA: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/gengit/FRAMA/HEAD/FRAMA -------------------------------------------------------------------------------- /LICENCE.txt: 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