Various utility- and helper-functions for sequence alignments and comparative structure prediction.
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int | vrna_aln_mpi (const char **alignment) |
| Get the mean pairwise identity in steps from ?to?(ident) More...
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vrna_pinfo_t * | vrna_aln_pinfo (vrna_fold_compound_t *vc, const char *structure, double threshold) |
| Retrieve an array of vrna_pinfo_t structures from precomputed pair probabilities. More...
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char ** | vrna_aln_slice (const char **alignment, unsigned int i, unsigned int j) |
| Slice out a subalignment from a larger alignment. More...
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void | vrna_aln_free (char **alignment) |
| Free memory occupied by a set of aligned sequences. More...
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char ** | vrna_aln_uppercase (const char **alignment) |
| Create a copy of an alignment with only uppercase letters in the sequences. More...
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char ** | vrna_aln_toRNA (const char **alignment) |
| Create a copy of an alignment where DNA alphabet is replaced by RNA alphabet. More...
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char ** | vrna_aln_copy (const char **alignment, unsigned int options) |
| Make a copy of a multiple sequence alignment. More...
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float * | vrna_aln_conservation_struct (const char **alignment, const char *structure, const vrna_md_t *md) |
| Compute base pair conservation of a consensus structure. More...
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float * | vrna_aln_conservation_col (const char **alignment, const vrna_md_t *md_p, unsigned int options) |
| Compute nucleotide conservation in an alignment. More...
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int | get_mpi (char *Alseq[], int n_seq, int length, int *mini) |
| Get the mean pairwise identity in steps from ?to?(ident) More...
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void | encode_ali_sequence (const char *sequence, short *S, short *s5, short *s3, char *ss, unsigned short *as, int circ) |
| Get arrays with encoded sequence of the alignment. More...
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void | alloc_sequence_arrays (const char **sequences, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss, int circ) |
| Allocate memory for sequence array used to deal with aligned sequences. More...
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void | free_sequence_arrays (unsigned int n_seq, short ***S, short ***S5, short ***S3, unsigned short ***a2s, char ***Ss) |
| Free the memory of the sequence arrays used to deal with aligned sequences. More...
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Various utility- and helper-functions for sequence alignments and comparative structure prediction.