2023-09-19: PETfold v2.1 -> PETfold v2.2; PETcofold v3.3 -> PETcofold v3.4 * Fix few memory leaks * Fix option --settree: ML tree is no longer calculated if tree is given; labels starting with digits are now allowed * Return length-normalized ensemble diversity: ( \sum{i,j>i+3} p_{i,j} * (1 - p_{i,j}) ) / ((gapfree-length-3)*(gapfree-length-4)/2) * update typedef struct definition to make compatible with gcc (Debian 10.2.1-6) 10.2.1 20210110 * Fix access of unallocated memory during parsing of some input trees 2017-09-13: PETfold v2.0 -> PETfold v2.1; PETcofold v3.2 -> PETcofold v3.3 * Change Makefile such that ViennaRNA Package CFLAGS and LDFLAGS are retrieved from pkg-config instead of hard coding them (thank Ronny L) * Fix invalid access to phyl->root->child->brother after releasing memory of phyl->root (thank Ronny L) * Fix several compilation warnings 2013-05-20: PETcofold v3.1.4 -> PETcofold v3.2 * PETcofold comes together with PETfold v2.0 as C version using Vienna RNA Package library and Pfold library * PET reliabilities are returned including gap-columns (parameter --ppfile) * parameter --setdelta replaces -setpetcon * parameter --setgamma replaces -setpartprob * rename "Normalized Score" to "Score" (like in PETfold) * remove parameter -LP 2013-05-20: PETcofold v3.1.3 -> PETcofold v3.1.4 * thermodynamic partial probability is calculated by sequence number normalized delta G's (before non-normalized) * calculate unpaired thermodynamic cofold-probabilities before adjustment by partprob (switch functions get_prob_unpaired_seq and multiply_partprob_paired; in older version unpaired thermodynamic cofold-probabilities were adjusted twice by partprob) * set RNA(co)fold option '--noLP' by default (same as in PETfold) and replace parameter -noLP by -LP * for RNAfold in function get_fasta_file, bases in gap-free sequences are only constrained as base paired when pairing partner isn't a gap * solve stem extension bug where base pairs get constrained that aren't connected with the constrained stem * now also for SETSTRUC: merge intramolecular reliabilities for bases with large intramolecular basepaired reliabilities and intermolecular reliabilities for the other bases * delta (petcon) is set back for the second alignment 2013-05-20: PETfold v2.0pre -> PETfold v2.0 * reads PPfold calculated reliabilities from STDIN (parameter --ppfold) to replace slow Pfold calculations for large alignments * check for valid alignment as input (sequences of same length) * PET reliabilities are returned including gap-columns (parameter --ppfile) 2011-11-07: PETcofold v3.1.2 -> PETcofold v3.1.3 * add parameter --setstruct for entire duplex structure which set partial structure bp-reliabilies to step1 bp-reliabilities * rename "Reliability" to "Normalized Score" (like in webserver) * don't break identifiers at 1st dot (like in webserver)