bug fix release

• invalid values in tree average (computed during root optimization) caused errors. These were due to singularities when the root was placed on a terminal node. This is now guarded against.
• more specific error message for invalid values.

small bugfix release

This release

• fixes problems with trees that lack branch lengths (thanks @trvrb)
• makes integer divisions explicit to avoid warnings.

Site-specific substitution models and new docs pages

This release introduce to major changes:

• documentation is now hosted on readthedocs at https://treetime.readthedocs.io/en/latest/
• TreeTime now allows for site specific substitution models. It can both infer site-specific substitution models (given sufficient data) and evolve sequences using site specific substitution models.

Other changes include:

• relaxed version requirements for matplotlib (supporting version 3 for python >3.6)
• various little bug-fixes
• some documentation of the sequence evolution capabilities.

fix handling of ambiguous sites in edge cases

This release is part bug-fix and part adding functionality to allow recovery of ambiguous bases for Fasta input (previously only available for VCF input).

• Fix handling of ambiguous sites in compressed alignment, see PR#87 for a detailed description.
• Enabling Recovery of Ambig Sites for Fasta-Input
  recover_var_ambigs() function has added functionality so that when called it not only recalculates the mutations, but also replaces node.sequence with a reconstructed sequence that includes ambiguous bases present in the original.

VCF reference case fix

This small release only fixes necessary upper case conversion for the vcf reference sequence.

Clean-up of rerooting mechanisms

This release consolidates the rerooting mechanisms into min_dev, least-squares and oldest. In addition, the command-line tools now accept lists of nodes or a single node as outgroup. Whether covariation due to shared ancestry is accounted for during rerooting can be controlled by the additional flag --covariation. Other changes include:

• tip-slack, variance associated with tips in covariance-aware regression, is now exposed to the command line as --tip-slack
• by default, commands don't account for shared ancestry covariance as this was causing issues in densely sampled trees.
• updated comments and help texts surrounding rerooting. Previous rerooting mechanisms still work but will print a deprecation message.

performance enhancements and bug fixes

This release speeds up some integral parts of treetime that should reduce the time needed for ancestral reconstruction and time tree inference by 30-40%. In addition, this release fixes a problem in the backpropagation of the marginal sequence likelihoods.

bug fix and minor feature additions

This release fixes a number of bugs, cleans up interfaces, allows to disable the use of phylogenetic covariation correction during rate estimation, and implements a number of minor features. Specifically:

• allows specifying a number constant sites not present in the alignment
• allow parsing of ambiguous dates from a pair of floats as in [2013:2016.7]
• allow the user to switch on/off tip labels in the time tree plots and allow fractional years
• fix issues with amino acid model and add flag --aa to force amino acid alphabet.
• fix interface for relaxed clock models and add export of branch-specific rates
• adds a rudimentary check of whether the alignment is consistent with the alphabet

bug fix and rate variation.

This release fixes a problem during output of results from the clock command line tool. In addition, we added functionality to incorporate uncertainty in the evolutionary rate into the confidence intervals of inferred dates.

subcommands and covariance aware rate estimation

This release exposes TreeTime functionality on the command line as treetime with a series of subcommands. In addition, the following aspects changed:

• the root optimization and rate estimation was factored out into a separate class TreeRegression.
• rate estimation is covariance aware assuming a multi-variate Gaussian distribution of the root-to-tip distances
• note that this covariance aware estimation can be thrown off by model violation. Hence filtering is essential and some extra slack (currently 10 mutations) needs to be added to the variance of root-to-tip distances
• the TreeTime.run method got streamlined.
• TreeTime now includes a method to parse dates from tables.
• data and exampled got moved out into a separate repo
• tests include vcf.
• the date constraints attached to nodes were renamed from numdate_given to raw_date_constraint
• a number of other small adjustments.