Skip to content
Browse files

version 6.3.0

  • Loading branch information
trvrb committed Feb 13, 2020
1 parent 12c1720 commit bd73cd670add721d73659355850540e80aefe306
Showing with 31 additions and 1 deletion.
  1. +30 −0
  2. +1 −1 augur/
@@ -3,6 +3,36 @@
## __NEXT__

## 6.3.0 (13 February 2020)

### Features

* Augur `refine`, `ancestral` and `traits` now use the
[upgraded TreeTime v0.7](
This should have a number of under-the-hood improvements.
[See PR 431](
* ancestral: New options to either `--keep-ambiguous` or `--infer-ambiguous`. If using
`--infer-ambiguous` the previous behavior will be maintained in which tips with `N` will have
their nucleotide state inferred. If using `--keep-ambiguous`, these tips will be left as `N`.
With this upgrade, we are still defaulting to `--infer-ambiguous`, however, we plan to swap
default to `--keep-ambiguous` in the future. If this distintion matters to you, we would suggest
that you explicitly record `--keep-ambiguous` / `--infer-ambiguous` in your build process.
[Also part of PR 431](
* traits: Allow input of `--weights` which references a `.tsv` file in the following format:
division Hubei 10.0
division Jiangxi 1.0
division Chongqing 1.0
where these weights represent equilibrium frequencies in the CTMC transition model. We imagine the
primary use of user-specified weights to correct for strong sampling biases in available data.
[See PR 443](

### Bug fixes

* Improvements to make shell scripts run more easily on Windows.
[See PR 437](

## 6.2.0 (25 January 2020)

### Features
@@ -1 +1 @@
__version__ = '6.2.0'
__version__ = '6.3.0'

0 comments on commit bd73cd6

Please sign in to comment.
You can’t perform that action at this time.