EXONERATE TEST DATA FILES
=========================

This directory contains various data files for testing the
Exonerate-related code in Biopython. All files are grouped by
Exonerate release version, from the most recent first.

Exonerate 2.4
-------------
exn_24_m_protein2genome_revcomp_fshifts.exn
exn_24_m_protein2genome_revcomp_fshifts_cigar.exn
exn_24_m_protein2genome_revcomp_fshifts_vulgar.exn
exn_24_m_protein2genome_met_intron.exn
exn_24_m_protein2genome_met_intron_cigar.exn
exn_24_m_protein2genome_met_intron_vulgar.exn


Exonerate 2.2
-------------
exn_22_m_affine_local.exn           affine:local model alignment
exn_22_m_affine_local_cigar.exn     affine:local model alignment, cigar lines
exn_22_m_affine_local_vulgar.exn    affine:local model alignmen, vulgar lines
exn_22_m_cdna2genome.exn            cdna2genome model alignment
exn_22_m_cdna2genome_cigar.exn      cdna2genome model alignment, cigar lines
exn_22_m_cdna2genome_vulgar.exn     cdna2genome model alignment, vulgar lines
exn_22_m_coding2coding.exn          coding2coding model alignment
exn_22_m_coding2coding_cigar.exn    coding2coding model alignment, cigar lines
exn_22_m_coding2coding_vulgar.exn   coding2coding model alignment, vulgar lines
exn_22_m_coding2coding_fshifts.exn  coding2coding model alignment, with frameshifts
exn_22_m_cigar_fshifts.exn          coding2coding alignment with cigar lines only, frameshifts
exn_22_o_vulgar_fshifts.exn         coding2coding alignment with vulgar lines only, frameshifts
exn_22_m_coding2genome.exn          coding2genome model alignment
exn_22_m_coding2genome_cigar.exn    coding2genome model alignment, cigar lines
exn_22_m_coding2genome_vulgar.exn    coding2genome model alignment, vulgar lines
exn_22_m_dna2protein.exn            dna2protein model alignment
exn_22_m_dna2protein_cigar.exn      dna2protein model alignment, cigar lines
exn_22_m_dna2protein_vulgar.exn     dna2protein model alignment, vulgar lines
exn_22_m_est2genome.exn             est2genome model alignment
exn_22_m_est2genome_cigar.exn       est2genome model alignment, cigar lines
exn_22_m_est2genome_vulgar.exn      est2genome model alignment, vulgar lines
exn_22_m_genome2genome.exn          genome2genome model alignment
exn_22_o_vulgar_cigar.exn           genome2genome alignment with vulgar and cigar lines only
exn_22_o_vulgar.exn                 genome2genome alignment with vulgar lines only
exn_22_m_ner.exn                    ner model alignment
exn_22_m_ner_cigar.exn              ner model alignment, cigar lines
exn_22_m_ner_vulgar.exn             ner model alignment, vulgar lines
exn_22_m_protein2dna.exn            protein2dna model alignment
exn_22_m_protein2dna_cigar.exn      protein2dna model alignment, cigar lines
exn_22_m_protein2dna_vulgar.exn     protein2dna model alignment, vulgar lines
exn_22_m_protein2dna_fshifts.exn    protein2dna model alignment, with frameshifts
exn_22_o_cigar_fshifts2.exn         protein2dna alignment with cigar lines only, frameshifts
exn_22_o_vulgar_fshifts2.exn        protein2dna alignment with vulgar lines only, frameshifts
exn_22_m_protein2genome.exn         protein2genome model alignment
exn_22_m_protein2genome_cigar.exn   protein2genome model alignment, cigar lines
exn_22_m_protein2genome_vulgar.exn  protein2genome model alignment, vulgar lines
exn_22_m_ungapped.exn               ungapped model alignment (default)
exn_22_m_ungapped_cigar.exn         ungapped model alignment (default), cigar
exn_22_m_ungapped_vulgar.exn        ungapped model alignment (default), vulgar
exn_22_m_ungapped_trans.exn         ungapped:translated model alignment
exn_22_m_ungapped_trans_cigar.exn   ungapped:translated model alignment, cigar
exn_22_m_ungapped_trans_vulgar.exn   ungapped:translated model alignment, vulgar
exn_22_q_multiple.exn               est2genome, multiple queries, multiple hits and hsps
exn_22_q_multiple_cigar.exn         est2genome, multiple queries, multiple hits and hsps, cigar lines only
exn_22_q_multiple_vulgar.exn        est2genome, multiple queries, multiple hits and hsps, vulgar lines only
exn_22_q_none.exn                   est2genome, single query, no results
