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CHANGELOG.rst

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Changelog

2.4.1

  • Unpin biopython now that pyvolve is updated.

2.4.0

  • Stop using matplotlib LaTex fonts in logo plots.
  • Pin biopython to <1.78 until Bio.Alphabet issues fixed in pyvolve. See here

2.3.9

  • Started testing Pep8 compliance with flake8
  • Removed deprecated scipy functions

2.3.8

  • Fixed bug in phydms_prepalignment due to mafft shortening sequence names.

2.3.7

  • Fixed scipy 2.0.0 deprecation warnings by using numpy functions in many places rather than scipy functions. See here.

2.3.6

  • Revert changes in 2.3.5, they led to numerical errors. Users will have to re-scale preferences when optimizations hits upper bound on parameter.

2.3.5

  • Increased maximum bound for stringency parameter as the max bound was too low and being hit during optimization in some cases.

2.3.4

  • Start testing with Python 3.6 and 3.7.
  • Remove use of deprecated Bio.Alphabet
  • Stop using deprecated natsort.natsorted

2.3.3

  • Fixed pandas deprecation bug.

2.3.2

  • Option for single color in logo plots.

2.3.1

  • Fix natural sorting of negative numbers in phydms_logoplot
  • Suppress matplotlib backend warnings.

2.3.0

  • Automate Travis tests
  • Only support Python 3.4+
  • Swapped basic and acidic colors of functionalgroup in weblogo.py

2.2.2

  • Fixed bug in spielmanwr

2.2.1

  • Fixed typo in phydms_comprehensive output file
  • Fixed normalization bug in Phi_x calculation, might slightly change numerical values for YNGKP models. This bug fix will generally slightly increase the log likelihoods for YNGKP models.

2.2.0

  • Changed computation of --omegabysite Q-values to compute them separately for omega > and < 1. This fixes the issue of many sites of negative selection leading to overly sensitive identification of positive selection.
  • Added utils.modelComparisonDataFrame function

2.1.4

  • Added spielmanwr calculation to ExpCM model
  • Fixed minor bug with overlays in weblogo.LogoPlot

2.1.3

  • Added scalebar option to weblogo.LogoPlot.

2.1.2

  • Fixed --colormap option to phydms_logoplot.
  • Added underlay and wildtype overlay bar options to weblogo.LogoPlot.

2.1.1

  • Altered setup.py to enable installation without numpy being pre-installed.

2.1.0

  • Added --gammabeta option to phydms
  • Added ExpCM with divpressure to simulate.py.
  • Updated citation
  • Fixed bug in simulate.py that caused incorrect branch length scalings
  • Change installation recommendations
  • Fixed installation of cython extensions.

2.0.5

  • Added --opt_details argument to phydms
  • Tweak to likelihood optimization convergence tests

2.0.4

  • Minor tweaks to phydmslib.simulate
  • Fixed rare bug in likelihood optimization that caused nothing to be optimized

2.0.3

  • Changes to reduce problems with convergence in --diffprefsbysite

2.0.2

  • Added new simulation capabilities to phydmslib.simulate
  • Added --initparams option to phydms
  • Modified --omegabysite fitting to reduce (hopefully eliminate) rare errors

2.0.1

  • Handle stop codons in preferences
  • Change default color scheme for logoplots
  • Some minor tweaks to reduce underflow
  • Some minor doc updates

2.0.0

  • Compatible with either Python 2.7 or Python 3.4 or greater.
  • Completely re-write of the implementation the likelihood calculations. We eliminate the dependence on Bio++ and instead use custom coded calculations without derivatives.
  • All tree topology inference is eliminated, some options are removed, numerical values are expected to be slightly different, and speed should be greatly enhanced.

1.3.dev0

  • Added --divpressure option for analyzing diversifying pressure at sites.
  • Added --fixationmodel option to allow different ways to relate preferences to fixation probabilities.
  • In phydms_prepalignment: bug fixes, have mafft use all available threads, and keep seqs in --keepseqs regardless of identity to refseq.
  • Added phydms_testdivpressure

1.2.5

  • Bug fix in phydms_prepalignment
  • Added more recent version of Bio++ code

1.2.4

  • Added phydms_prepalignment program.

1.2.3

  • Updated docs
  • Handle negative MRCAs for --dateseqs without error
  • Added option --colormap to phydms_plotselection.
  • Removed requirements that input sequences be unique in alignment.

1.2.2

  • Fixed bug in handling YNGKP_M7 model in output of phydms_comprehensive
  • Added option --ncats option to set the number of categories for the distributed omega in the YNGKP_M7 and YNGKP_M8 models.
  • Fixed bug in --ngammarates that caused only one rate to be used.

1.2.1

  • Eliminate negative branch lengths to avoid bug in biopython (<= version 1.66) at parsing them.

1.2.0

  • Updated Bio++ again.
  • Added --dateseqs option phydms and phydms_comprehensive.
  • Fixed bug that was making YNGKP models always use --fitF3X4 option.
  • Added YNGKP_M1 and YNKGP_M2 models.
  • Changed meaning of --yngkp option to phydms_comprehensive to allow multiple or no models beyond YNGKP_M0.
  • Added --gammarates option to phydms and phydms_comprehensive.
  • Added env test to ./tests/
  • Changed source code and docs url from jbloom to jbloomlab account on GitHub.

1.1.0

  • Updated to newest versions of Bio++
  • Added --yngkp option to phydms_comprehensive, and changed default from YNGKP_M3 to YNGKP_M8.
  • Added --useLog as option to phydms and phydms_comprehensive, and made differential preferences automatically try logarithms when it encounters problems.
  • Added --avgrandcontrol option to phydms_comprehensive.
  • Disallowed identical sequences in alignment.
  • Updated to newer versions of Bio++
  • Added output for site likelihoods to log file under the fixed stringency parameter when using --stringencybysite.
  • Fixed --no_optimize method for YNGKP_M3, YGNKP_M7, and YNGKP_M8 by making program use the old likelihood method for these models.

1.0.2

  • Fixed bug in file checks for --no_optimize option to phydms
  • Add --no_avgprefs option for phydms_comprehensive

1.0.1

  • Included __* files in Bpp in MANIFEST for proper PyPI / pip installation

1.0.0

Initial release