• fix infer_ancestral_sequences silently falling back to joint reconstruction instead of marginal in all iterations after the first when branch_length_mode='marginal' issue #601 PR #602

• fix treetime clock not writing molecular_clock.txt with the rate estimate, despite documentation listing it among output files. Also fix copy-paste message in treetime timetree that said "Inferred sequence evolution model" for the molecular clock file. Reported by @1ucyb issue #574, fixed by @ivan-aksamentov PR #575
• drop Python 3.7 from supported versions

• fix fill_overhangs filling terminal gaps with N (asparagine) instead of X (ambiguous) for amino acid sequences by @jbloom issue #522 PR #523
• fix crash when combining branch_length_mode='marginal' with stochastic_resolve=True. Reported by @jameshadfield issue #516, fixed by @ivan-aksamentov PR #517
• fix KeyError: 1 when loading mugration weights CSV with pandas 3.x by @ivan-aksamentov PR #518

• fix output of mutations into the branch_mutation.txt file which was masked by a conditional
• adjust CLI help
• adjust output precision

• calls to some random number generator error-ed after the recent switch to treetime owned RNGs.
• default argument for clock-filter method had a spelling mistake
• a branch length optimization function didn't handle profiles==True correctly

0.11.2: improvements in VCF parsing/writing + clock-filter functionality

• rewrite of the vcf reading and writing code including many more tests, closer alignment with spec, and performance improvements by @jameshadfield PR #263
• clock-filter command can now remove detected outliers with the additional flag --prune-outliers.

Bug fixes and tweaks to plotting

• fix division by zero error during GTR inference
• improve doc strings in parse dates
• tweaks to background shading in timetree plot function (plot_vs_years)
• allow to specify branches on which date confidence intervals are shown.

Feature: Better clock-filtering

Previously, only a crude analysis of whether the divergence of tips roughly follows a linear trend was implemented. Tips that deviated too much from that regression line were flagged as outliers and this threshold was parameterized as number of interquartile distances of the distribution of residuals n_iqd. This filter is not very sensitive and often misses misdated tips that severely distort the tree but still fall within the distribution of root-to-tip distances at that time. To overcome this, we implemented a novel filtering method that fits a simple gaussian model of divergence accumulation. Information on outliers is saved in a pandas DataFrame self.outliers of TreeTime and written to file as a tsv file when running treetime as command line tool.

Other fixes

• error when rate estimate is negative during the rate susceptibility calculation. Give hint in error message to specify the rate and its uncertainty explicitly.
• Fix bug issue #250 introduced in 0.10.0 where treetime fails in absence of an alignment when trying to create an auspice json file. PR #251

• avoid probability loss at the end of the domain of distributions (addresses #242)
• fix erroneous check for merger model
• raise error when probability is lost.
• improve initial guess in branch length optimizations

• the output directory now contains a json file that is compatible with auspice.us. Both time scaled phylogenies and ancestral inferences can now be visualized and explored using auspice. Available colorings are "Date", "genotype", "Branch support", and "Excluded". See PR #232 for details.
• move most function related to IO of the command line wrappers into a separate file.
• make TreeTime own its random number generator and add --rng-seed to control state in CLI. Any previous usage of numpy.random.seed will now be ignored in favor of --rng-seed. See PR #234
• add flag --greedy-resolve (currently default) as inverse to --stochastic-resolve with the aim of switching the default behavior in the future.
  Add deprecation warning for greedy-resolve.
• tighten conditions that trigger approximation of narrow distribution as a delta function in convolution using FFT PR #235.
• Drop support for python 3.6.
• Don't attempt to show figure when calling Phylo.draw to suppress matplotlib back-end warning.