Maintenance updates
- Update the Catch testing framework to version 2.13.10
- Replace deprecated use of bind2nd to support recent C++ compilers
Version 2 of LocARNA introduces several improvements that make LocARNA faster and easier to use. Most prominently, it features a novel sequence envelope heuristic in all major alignment modes, which significantly improves over less sophisticated banding heuristics (in terms of speed, robustness, /and/ flexibility). Most directly notable for users, it changes the default parameters to more appropriate settings. In addition to various detailed improvements of the LocARNA tools, there are significant changes under the hood: the C++-code of the LocARNA library was simplified and modernized making use of C++-14 features. These changes make the library easier to use, maintain and extend.
The development of version 2 extended over numerous 'release candidates' that not only fixed bugs and stabilized features, but - despite their RC designation - also introduced some new functionality e.g. (for clustering and benchmarking). Comprehensive change log is therefore provided for the sinlge release candidate releases.
- Improve readme
- Update doxygen documentation
- Fix: add conda-forge channel in conda install
- Add CLUSTAL-header in realign example
- Use full names in tRNA_5 example
- use doxygen awesome style
- use REAMDE.md as main page in docu
- Reformat changelog and include in docu
- include man pages from perl scripts and C++ programs
- Reformat help output of C++ programs
- Activate doxygen pdf docu
- Reformatting in mlocarna pod
- Update email address
- Remove build status
- Make mlocarna less chatty
- mlocarna: Catch empty names in fasta input + modify output in case of duplicate names
- mlocarna: Catch missing clustal header in realignment input
- turn off warning about unsupported nucleotides
- Add benchmark plot script to compare multiple experiments
- Add alignments target in benchmark Makefile
- Keep input file in realignment mode as input.aln
- Fix pp2dot
- Fix reliability output (aligned offsets/name widths)
- Fix mlocarna option width in probabilistic mode
- Fix dependency in benchmark makefile
- Fix behavior of verbose mode / printing of consensus structure
- fix and support png/svg output in benchmarking
- Fix: use reference type for loop var
- Fix bug: quote names in newick trees
- Fix buffer size
- Update configure.ac by autoupdate
- Strip -fno-lto from Vienna RNA configured VRNA_LIBS
- doxygen: Turn off autolink support
- Require Vienna RNA 2.5.1
- Update tests
-
The calculation of the guide tree is rewritten; in consequence mlocarna is now more useful for clustering RNAs, since score distances are reported in the tree output (as well as names that correspond to intermediate alignments of subsets of the input sequences in subtrees)
-
Generally, improved functionality for multiple alignment
- better support for 'clustering' use case
- distances and inner node labels in newick output
- inner node labels correspond to names of intermediary alignments
- introduces new perl Tree class with internal full tree representation
- supports flexible traversals, filtering, etc
- parsing and writing newick format fully supported
- handles multi-ary trees
- assign meaningful indices to intermediary alignments from most closely related to further apart
- changes naming scheme of intermediary alignments in iterative alignment (include round in name)
- better support for 'clustering' use case
-
Perform distance-based upgma for guide tree computation: Calculate distances from locarna scores as distance = max_score - score
-
Add option (max-alignment-size) to limit the size of computed multiple alignments
-
Don't write am and bm probabilities by default; introduce options to control writing.
Motivation: probabilities require lots of disk space, which is rarely used for inspection or further processing
Introduces new options
- --write-probs / --no-write-probs
- --write-am-probs / --no-write-am-probs
- --write-bm-probs / --no-write-bm-probs
All of them default to 'no-write'
- Improve man pages (add dois, slightly edit)
- Include disclaimer about the use of many threads in mlocarna man page
- Improve documentation of small tools (add missing man page includes)
- Add locarna_mcc man page
- Fix quoting in newick trees
- Update script mlocarna_nnames
-
Refactorize guide tree computation.
-
Inform user that results were written to target directory
-
Code cleanup: Cleanup reference variables Cleanup amprobs/bmprobs hash references Cleanup sparse matrix module, return hash refs Change global var %opts to hash reference Expand leading tabs Cleanup in MatchProbs module Cleanup threaded/unthreaded modules Cleanup match probability computation. Remove redundant code for sequential computations of already parallelized steps
-
Avoid unnecessary cloning of hashs; cleanup shared cloning
-
factorize: introduce name normalizer class
- Remove obsolete script to label trees
- Update CARNA server related scripts
- Slightly simplify make of man pages (require man_include files)
-
Fix bug in sequence trace probability computation, which was potentially critical for large instances (e.g. aligning sequences with ~1000 length difference)
-
Remove superfluous output of alignments in probabilistic mode
- Update travis CI script
- Fix initialization order [FitOnOff]
- Fix missing and superfluous headers [alphabet.hh/icc]
- experimental extension of boundary prediction by position wise penalties, can use consistency file information [reliability-profile.pl, locarnap_fit]
- Accept empty sequences in input
- Re-enable computing consensus structures in mlocarna output and stk-files
- Remove perl prototype specs to avoid perl 5.18 incompatibility
- Adjust behavior of locarna and mlocarna for pairwise alignments
- do not use alifold in binaries when calculating base pairs for single sequences
- use noLP in mlocarna for calculating base pair probabilties /and/ the alignment
- increase output precision for probabilities in pp files (reducing rounding issues for the typical cutoff)
- Allow penalized in global alignment
- Fix kbest HIT line
- Fix static linking (with gomp)
- Remove one extra line after CLUSTAL header (which used to be written by mlocarna)
- Fix kbest alignment (allow and detect empty alignments)
- Fix local end output (HIT line) for non-local alignments
- Add stopwatch (for consensus computation)
- Introduce parameter --consensus-gamma for mea consensus 'gamma'
- Class Alignment handles start and end position for non-local alignments; methods local_start(), local_end() of Alignment are replaced by start_positions(), end_positions()
- Fix free endgaps bug (negative alignment scores were handled incorrectly)
- Fix empty anchor constraint (correctly recognize/report when anchors are specified)
Both improvements were introduced to handle large instances
- Improve alifold consensus computation - turn off by default (also speeds up mlocarna) - handle cases where consensus is not/cannot be computed - warn if consensus is not computed / fail if explicitely required (pp) - handle recomputation of consensus if file/screen output differ (local out)
- Support sequence envelope computation with extended precision - set the default to extended precision - recognize failing partition function calculation - (for sequence trace and match probabilities) - extend LocARNA's quadmath.hh header and simplify its use - use templates for partition function type - support extended (long double) and quad precision (float128)
-
Sequence envelopes for locarna, locarna_p and sparse;
- Compatible to anchors, local alignment, and free endgaps
- New parameter: --min-trace-probability (on by default)
- Refactor class MatchProbs -> EdgeProbs and sub-classes; improve interface and docu
- use sequence envelopes by default
-
Change default parameters for scoring (new gap cost and tau factor)
-
Support higher precision floating point arithmetic for locarna-p
- pf calculation (long double and quad math) selectable dynamically without recompiling
- support extended (long double) and quad precision (quadmath)
-
Support caching of pp files (--dp-cache)
-
Support in-package benchmarking (measuring sps, sci, and mcc)
- Avoid shell evaluation in mlocarna system calls
-
Modernize and restructure code Transition to C++14 standard: use of unique_ptr, auto types, range loops, template meta programmin using type_traits, ... Systematic clean up of the library classes Introduce named arguments; zip and enumerate iterators Improved organization of command line help; reduce redundancies Improve handling of format and annotation types in MultipleAlignment
-
Optimize inner loop: add sentinels to left and right adjacency lists
-
Reduce memory footprint of locarna
-
Anchor constraints restrict trace controller
-
Refactor computation of input pp files [mlocarna]
-
Use locarna_rnafold_pp for constrained folding [mlocarna]
-
Update travis CI test
- Fix specifying anchor constraints via bed file [mlocarna] allow arbitrary order of entries in bed input
- Fix ribofit code (make experimental ribofit scoring usable)
- Fix confusion matrix: count_common_bps()
Improve consensus dotplot computation (avoid accumulation of low
probability base pairs)
Some cleanup
1.9.2pre4
Fix left and rightmost anchors (fixed local alignment); add unit tests
Optimize maximization in innermost loop
Add unit and program tests
1.9.2pre3
Make consensus structure / dotplot types independent [option
--consensus-structure alifold (current default) used to also
determine the computation of consensus dotplots. The consensus
dot plot is now independent (new default: no alifold consensus
dot plot).]
fix strict semantics for anchor constraints
fix compatibility '--keep-sequence-order' with anchor constraints
1.9.2pre2
mlocarna: write ps files (aln.ps, alirna.ps and if probabilistic,
alidot.ps) from alifold call on result alignment to the
results output directory;
use alifold options --aln --color --mis
fix mlocarna: find pw-aligner and pw-aligner-p executables in PATH
improve help and man pages for locarna, locarna_p, sparse;
refactor code for help text (string map for help text)
write text inserts for man pages, which are autogenerated from help
fix bug in reading stockholm anchors
remove parameters min_am_prob and min_bm_prob from locarna
and sparse CLIs;
they are useful only for locarna_p
introduce strict semantics for anchor constraints
and make default (see mlocarna --relaxed-anchors)
fix exparna_p output
add mlocarna option to realign; support 'consensus'
constraint specifications
add mlocarna option to load (default) configuration from file
add mlocarna option to read anchor constraints from
bed-format specification
add option --maxBPspan (analogous to ViennaRNA's maxBPspan)
activate penalized option for mlocarna
update documentation of mlocarna
update reliability-profile.pl: suppress too verbose output;
improve behavior of subseq option
Tests:
introduce mlocarna test with comparison to reference results
- generate reference results with make gen-test-results
add stockholm writing test
Bug fixes:
catch empty sequence case for alifold
fix error message concerning max-diff-aln in mlocarna
fix mlocarna bug: write stockholm also in probabilistic mode
fix mlocarna error handling when running multithreaded
fix doxygen/docu generation
Add checks: multi-threaded mlocarna, locarnate
Fix severe problem with threads in mlocarna, which caused hangs
Fix mlocarna with sparse (precomputation of inloop probs)
Update VRNA/C11 configuration (adapts automatically; remove --enable-STDC )
Require ViennaRNA >=2.3.1
Improved options help
Cleanup some files in the repository and distribution
Add configure flag --enable-STDC; set default to C11 (RNAlib compatibility)
Fix output order of reliable structures in mlocarna
Migrate to new vrna api; fix pf_scale bug
Improve input checking in mlocarna
Increase API version to 1.5
Wrap long alifold consensus output in mlocarna
Add consensus structure in locarna output, selectable types mea|alifold|none
Add optional stockholm output to mlocarna
Introduce quiet switch for locarna, locarna_p, sparse, and exparna_p
Code cleanup in driver programs
Handle sequence name clashes by systematic renaming
Read stockholm format
Factorize common code in locarna, locarna_p and sparse (MainHelper)
Add stockholm support input and output to locarna
Fix bug occuring with empty input sequences
Call alifold with /best/ parameters (from perl /and/ c++)
Fix locarnate (compatibility to current locarna); add unit test
improve configuration
improve ubuntu packaging
fix anchor constraint check in mlocarna fasta input
allow ribofit for mea - e.g. for probabilistic; this used to require ribosum
adapt to and require ViennaRNA >=2.2.4
fix all static linking
link binaries statically to libLocARNA by default;
otherwise use --enable-dynamic-binaries
fix & clean up code (after cppcheck static analysis)
prepare for rpm packaging
prepare for Ubuntu packaging
fix man pages
- update generation (add missing man pages)
- fix program names
- improve/fix help/man of binaries and locarnate
clean exploc_p (get rid of "in"-mechanism)
fix problems in tests (make check) w/o enable-debug
remove wrong MultipleAlignment format check
remove locarna.pl from distribution (functionally replaced by binary)
remove unused parameter "width" from locarna_rnafold_pp
Increase API version to 1.4
Get rid of locarna.hh
In clustal(-like) alignment output, adapt formatting to long names
Improve libRNA config, in cases where pkg-config does not work:
allow compiling without libgomp, if libgomp is unavailable and
is not used by libRNA
Fix behavior in case structure constraints + local folding (see 1.8.2)
allow empty input sequences/alignments and fix related problems
fix score of local alignment w/ empty input sequences
fix potential overwriting of parameters in classes Aligner*,
which was observed only with gcc-5.2
fix bug that crashed printing string options in verbose mode
improve portability for easier installation on recent MacOS X:
compile without openmp; handle VRNA w/o pkgconf file
fix c++11 warnings; fix incompatibility with libc++
fix incompatibility with clang (now used by MacOS X); fix warnings of clang
remove g++ warnings
change semantics w.r.t. constraints + local folding:
constraints turn off local folding
reformat change log
support generating doxygen documentation from
distribution by make doxygen-doc
penalized alignment
experimental galaxy wrapper generation
implement ribofit
Bugfix in OMatrix: incorrect address calculation
Bugfix: LocARNA crashed while writing the result pp file if
alignments of zero length are computed with options local file
output and alifold consensus dp (alifold workaround)
bugfixes (OMatrix, alifold len 0 bug)
implement slide rule and conflict rule for f1 and mcc calculation;
also use default minimal base pair length 3 in class
ConfusionMatrix; class interface changes slightly
Remove absolute path dependencies in scripts. This changes the
behavior, since paths are not fixed at compile time. For
example, the Vienna RNA programs are located via PATH environment
variable.
Require linking to VRNA. Remove configure options. Disallow
renaming of Vienna RNA tools RNAfold, etc.; expect them in path.
Always compile SPARSE/ExpaRNA-P. Don't pass mlocarna script
through configure anymore.
Add option --sparse to mlocarna
Add rnafold-temperature option to mlocarna
Use rnafold temperature and parameter files for alifold
Warn if used with alifold-consensus-dp
Add unit tests for mlocarna calls (standard, prob, sparse)
Align alifold structure to alignment in mlocarna output
Add Example gcvT.fa for SPARSE
sparse: --special-gap-symbols option added (default is false)
max-bps/uil/bpil-length-ratio for SPARSE/ExparnaP
Second type of stacking terms: new-stacking
Add heuristic to restrict maximum number of "significant" base
pairs: max-bps-length-ratio
Add max-diff restriction at arc match ends: --max-diff-at-am
Restructure parameter passing to Aligner* classes: use "named
argument" idiom
ExpaRNA-P rename of tools
Fix bug concerning iterative alignment and alignment evaluation
Rename locarna_X to exparna_p
ExpaRNA-P code "publication ready"
Handle inconsistencies due to anchor constraints in conflict
with other constraints/heuristics, e.g. max-diff: 1) accept -inf
pairwise similarities for guide tree construction; 2) clear
consensus anchor strings with duplicate names
Fix bug. Quotes in fasta-names caused failure when
generating pps via locarna_rnafold_pp in mlocarna.
(1.7.3.1)
Resolve rnalib dependency. New configure option with-sparse
is now required to compile with ExpARNA-P and SPARSE functionality.
(1.7.5)
Merge in new sparsification related code.
Added fasta input check in mlocarna.
(1.7.6)
Small bug fixes
Fix memory leaks
Prepare alignment evaluation functionality
Code cleanup/refactorizations
(1.7.6.9)
Introduce configuration header config.h
Fix man page dependency problem
Make sure that make check and make distcheck work
Split RnaData into RnaData and RnaEnsemble
Introduce new version of pp format (2.0)
Read/write of inloop probabilities
Cleaner separation of reading/writing of alignments/probability data v.s. computation;
in particulare remove I/O from Alignment class
Cleaner handling of gaps, alignment edges, and gap symbols in I/O
New option --stopwatch (in locarna*) to turn on detailed internal timing
Change class Sequence to be a mere interface to MultipleAlignment that allows operator [] for column access
Make constraints optional part of multiple alignments; make write/readable with the alignment in clustal and pp format
Remove options anchorA, anchorB from locarna and locarna_X
Support anchor and structure annotation in MultipleAlignment
RnaEnsemble constrains the folding by structure annotation of
Multiple Alignment (if given)
(Release 1.7.7)
Support precomputing in loop probabilities for SPARSE
Fixed reading of PP 2.0
(Release 1.7.8)
LocARNATE: new code, improvements
Exparna-P: Suboptimal traceback and improvements
Change default behavior of mlocarna for sequence-local alignment: proceed
with only-local subalignments; options local-progressive and
global-progressive control behavior, where --global-progressive
reactivates the previous one.
(Release 1.7.9)
Newick bugfix
Small modifications for library use (e.g. for carna)
(Release 1.7.10)
Improve max-diff heuristic (without reference alignment): make
symmetric and always allow sufficiently large deviation
(Release 1.7.11)
Fix bug in locarna_rnafold_pp (reading clustalw from stdin)
Fix bug concerning structure constraints
Update format conversions in mlocarna to pp 2.0 format
Support for fixed structure constraints (directly in C++)
(Release 1.7.12)
Fix bug that compromised LocARNA-P w/ anchor-constraints in 1.7.12
In-loop support for fixed structure constraints
(Release 1.7.13)
Bugfix: computation of consensus anchor constraints could fail; now resolve
name clashs by selecting lexicographically smaller name.
(Release 1.7.13.1)
fix bugs in reliability plotting and "fitting"
(1.6.2.3)
New tool locarna-mea for computing the max. expected accuracy structure
from a dot plot
(1.6.2.4)
New features for pp2dot script
New script for generating average pp-files
In combination, generate nice colored dot plots;
used first for the output of the carna server
(1.6.3)
Merge with recent Exparna-P/locarna_X code
(1.7)
New classes for infinite integers (this is used for scores,
which can be -infty, i.e. undefined). The new mechanism automatizes
normalization of infinity using the type system and avoids wrong
usage by the type system. Consequently, it is more flexible. It avoids
a bug in normalized alignment and helps to clean up the Exparna-P code.
(1.7.1)
Add reading of score matrix in mlocarna
Fix bug in probabilistic mode, which did not allow '#' in sequence names
Fix bugs in output of score matrix
Fix drawdplin
Fix bug in trace controller
(1.7.2)
Add locarna_n code, alpha status
Fix a bug related to use of trace controller (max-diff) with free
endgaps.
Fix autodetection of input multiple alignment file format,
i.e. FASTA vs. CLUSTAL.
Change interface of scoring such that gapA (gapB) depends on only
positions in sequence A (B), resp.
(1.7.2.1)
Major improvements of the RnaData class and its interface
Some clean up
(1.7.2.5)
Some bug fixes, support for graph kernel guide tree
(1.7.2.6)
Include graph kernel guide tree support in mlocarna
(1.7.2.7)
Some cleanup, release.
Fix bug (missing initialization) in RnaData
(1.7.3)
Alignment in limited deviation to a reference alignment
program deviation computes deviation of alignment to reference
Deactivate max-diff-aln for --probabilistic/locarna_p
(Version 1.6)
Restructure code
library libLocARNA is generated and is used as library by executables
Fix name normalization bug in mlocarna.in
(Version 1.6.1)
Doxygen compiles without warning and produces useful documentation
of the library
Vienna RNA library is now required for compilation and will be linked
Locarna accepts clustal files as input and then computes base pair
probabilities via pf_fold of the Vienna RNA lib. Currently this is
limited to single sequence clustal files.
Implement reading of mfasta files (still switched off).
Implement several alignment comparison measures (and use in locarna_deviation) (EXPERIMENTAL)
Make linking to Vienna librna configurable, default=off! Activate
by calling ./configure with --enable-librna.
New strategy for consensus dot plot generation: employ RNAalifold
-p. Enable via mlocarna's option --alifold-consensus-dp Note: the
default consensus dot plot computation seems to be flawed! The new
tool pp2dot allows to visualize consensus dot plots (by converting
pp to Vienna-like dot plot postscript files) and should help to
improve the default strategy (otherwise we are going to replace
it!)
mlocarna accepts via --tree-file a super-tree as guide tree and
automatically projects to the taxa in the input.
Allow quotation in newick trees (using Text::ParseWords)
and use quotations when generating newick trees
Fix a problem with compiling on case-insensitive file systems (generate locarna.bin instead of locarna executable in src, rename at install)
add alifold-consensus-dp option for mlocarna
Add mlocarna options (pw-aligner and pw-aligner-p) to run
specified binaries in place of locarna and locarna_p. This can be
used to plug in compatible programs like carna
Bug fix; compilation without linking libRNA was broken.
release (1.6.2)
Bug-fixes: treefile regexp, LARGE_PF name clash mit Vienna package
(1.6.2.1)
add script to translate to normalized names for mlocarna
Add options pw-aligner-options and pw-aligner-p-options, to mlocarna to pass option strings to the pairwise
aligner. This is useful in combination with specifying
non-standard pairwise alignment programs.
Support generation of pp files from dp2.ps and dp.ps files when
skipping dot plot computation with --skip-pp (keep name for
legacy). This allows the combine user-defined dotplots with
anchor constraints from the mfasta input file.
Support fixed structures (with pseudoknots) in the fasta input
of mlocarna as structure constraint string with tag #FS
All base pairs in the fix structure receive a probability of 1.
(1.6.2.2)
new tool Utils/reliability-profile.pl generates nice
profile plots from mlocarna --probabilistic output directories
stacking turned off, unless exp-prob option used
(locarna-1.5a)
Add normalized local alignment, proof of concept
(locarna-1.5.1)
Combine normalized alignment and kbest
Introduce option better to enumerate suboptimal solution
better than given threshold
--kbest and --better can be used together
(locarna-1.5.2)
Fix build in separate build directory
Introduce new representation of fasta data
Major restructuring/refactorization of mlocarna.in and MLocarna.pm
Move many functions of mlocarna.in to packages and
introduce several new packages to group functions thematically
(locarna-1.5.3)
Resolve a bug that made LocARNA handle Ts as unknown
characters. LocARNA now automatically transforms Ts to Us in input
sequences. The bug did not affect input sequences without Ts. For
matchs involving Ts, LocARNA wrongly used an ad-hoc score instead
of the ribosum score for matches involving 'U', as one would
expect.
Add EdgeController: adds feature to constrain (max-diff-match)
alignment relative to a given alignment. Change handling of
max-diff-match in case of unequal length: instead of relaxing
constraint, change constraint to |i*(lenB/lenA)-j|<=max-diff
Add multiple alignment class to support construction of EdgeController.
Change Copyright to GPL v2 and update README
rename max-diff-match to max-diff heuristic.
replace EdgeController by TraceController use the max-diff delta
( TraceController ) to restrict alignment of paired and unpaired
positions (not only ends of arcs) in Aligner. Semantics is given by
restriction of alignment cuts/matrix cells!
iterative alignment using SCI as optimization criterion
cleanup mlocarna code
cleanup mlocarna output (inclusive output modes -v, --moreverbose)
improve reliability computation
multi-threaded mlocarna, new option --cpus <n>: use n threads
more structure for mlocarna output to file system (distribute
files to subdirs)
introduce --pf-scale parameter to locarna_p and mlocarna
precompute exp base match similarity and gap cost for partition
function => significant speed up of locarna_p
change handling of max_diff: guarantee at least |lenA-lenB|
improve outside algorithm in locarna_p (reduce sizes of Mrev-matrices)
=> with prior optimization massive speedup of locarna_p
add probability filtering after cbt
further improvement of outside (cheaper computation of certain
Mprime entries)
iteration with reliable structure as constraints
(option --it-reliable-structure)
support for non-threaded perl
fix some problems with the option parsing
(e.g. now -p=0.1 is correct and -p=a throws an error)
fix bug in initialization for structure locality
change semantics of constraints in the context of locality:
anchor constraints (i,j) now enforce that edge (i,j) is part
of the local alignment (for sequence and structure locality)
add missing options to mlocarna, fix bug in locarnate (thanks to Wolfgang)
fix bug with sharing/threads in mlocarna (v1.4.6)
locarna_p computes probabilities for matching fragments
clean manpage of mlocarna
offer large data type "long double" for partition function
computation. this is available when configuring through option
--enable-large-pf. Use this in case of long alignments, where the
partition function exceeds the range of type "double". Although
--pf-scale sometimes provides a workaround, for multiple alignment
of large sequences it is often the only viable choice.
add free endgaps via option --free-endgaps "----", for locarna
gaps at all for ends can be allowed for free independently.
For mlocarna, --free-endgaps will allow free end gaps at any end.
fixed serious bugs concerning stacking: due to these bugs,
mlocarna did not profit from stacking and locarna could get wrong
results with stacking turned on.
Change base pair filtering by probability for stacking: ignore
stacking probability, filter only by base pair probability.
(locarna-1.4.9alpha)
remove bug in anchor constraints
Ribosum-85-60 compiled in
changed default parameters to something reasonable
remove bug in rna_data.cc reading dp.ps, v 1.2.4
change char * to std::string in options module
(the g++-compiler does not like it anymore :))
integrate locarnate - a tool for multiple alignment
that uses locarna in combination with tcoffee
(Version 1.3)
partition function version of locarna (locarna_p)
experimental support for multiple alignment using
basematch probabilities and probabilistic
consistency transformation
(Version 1.3.2)
mlocarna can write basematch probabilities for plotting
plotting of basematch probs (Utils/plot-bmprobs)
mlocarna now correctly accepts input trees in newick-format that
are terminated by ";". However, it does not enforce the ";"-termination
mlocarna now writes the result.tree in ";"-terminated newick-format
use rounding (instead of truncate) in scoring module, when
converting from double to score_t. This fixes some inconsistency
between 32/64bit and is the correct thing to do anyway
improve speed up gained from using anchor constraints
add probabilistic scoring with consistency transformation
with structural scoring in progressive alignment steps
change options of mlocarna for probabilistic/mea-type alignment
refactoring; new classes Scoring, RnaData, ...
preparations for better scoring:
reading Ribosum-Data, new class Ribosum
computing match probabilities in sequence alignment (Gotoh):
Implemented methods: pairHMM, partition function, local pf
new class MatchProbs
improve option parser: introduce sections and section hiding
integrate new scoring scheme: maximum expected accuracy
significant speed-up due to re-organization of the recursion
equations:
redefine D to already contain the score contribution of
the arcmatch. This reduces these computations by orders of
magnitude!
add constraints to pairwise and multiple alignment. This means
for locarna: integrate anchor constraints
for mlocarna: read and pass structure constraints to RNAfold -p,
read and pass sequence constraints to locarna
The pp-format is redefined in order to pass constraint information from
mlocarna to locarna.
New class for representing and calculating with infinite scores
changed default sequ-local=on to off
increased min_prob in mlocarna.pl
bug fix in computation of consensus probs
rewrite noLP
add (pseudo)affine gap penalties
make mea working
change default output width to 120
ribosum scoring for classic score
change handling of options in mlocarna
mlocarna learns iterative refinement
mlocarna learns conistency based transformation
true affine gap cost (implemented using additional vectors E and F)
implemented stacking (v_1_2alpha)
removed bugs in traceback
cleaned options
include version name in output (v_1_2_1a)
add man pages
add Ribosum85-60 matrix in distribution
avoid writing to global /tmp directory (v_1_2_2a)
avoid potential file name conflicts in mlocarna
accept duplicate (or not prefix unique) names in mfasta input
add support for aligning alignments
(used for multiple progressive alignment)
Lower memory consumption of locarna.
In particular important in case of
scanning (target against genome)
Add some options/features that are useful for scanning
option --kbest
option --max-diff-am
option --ungappedA
option --local-output
handling of nucleotide-symbol N for unknown in input
add support for stacking alignment, not finished
small changes, rename mlocarna-p to mlocarna
global alignment
extension to local alignment (sequence+structure locality),
no_lonely_pairs option
command line options
recognize and read dot.ps files (in add to formerly used pp-files)