Feature+&+Bug+History

= = Here are some of the more notable new features and bug fixes since version 1.0. If the previous way Zephyr worked could have yielded errors in substantive results (e.g., there was a bug in a phylogenetic calculation) are marked with.

There is also a list of release dates.

New features or bug fixes to be included in next release of Zephyr
New Features
 * IQ-TREE support added.

Bug Fixes
 * None yet.

Version 2.01
New Features
 * Added ability to adjust maximum run time for CIPRes runs. Build 90.

Bug Fixes
 * PAUP Neighbor-Joining was broken in multiple ways. Fixed in build 87.
 * Zephyr failed in several ways under old (pre-1.8) versions of Java. [Thanks to David Kavanaugh for the report.] Fixed in build 88.
 * TNT runs failed in Linux. [Thanks to Mario Cozzuol for the report.] Fixed in build 89.
 * RAxML runs in which outgroups were specified failed. Fixed in build 91.
 * Several small bugs fixed.

Version 2.0
New Features
 * Support for the **CIPRes** REST services. This allows you to start a run on the CIPRes cluster from within Mesquite. Zephyr will then harvest the results once the CIPRes run is completed. You will need an account on the CIPRes REST system. Initial implementation is for RAxML and GARLI only.
 * Automatic **parametric bootstrapping** through implementation of the **SOWH test**.
 * Direct connections to external programs allowing Mesquite greater control over those programs.
 * More extensive support for PAUP, including likelihood, distance, and SVD quartets analyses.
 * Support for the --mesquite flag in RAxML 8.1.4 and later in runs on the local computer
 * Live view of trees in RAxML 8.1.4 or later when doing multiple non-bootstrap runs
 * Saving of trees from partially completed runs (in some circumstances).
 * For GARLI searches, you can set the character evolution model to be used by entering the name of the model from Posada (2008) using the Set by Model Name... button in the dialog box. For example, if you enter "TIM2e", then Zephyr will automatically set the rate matrix to "Custom", with the substitution code as "(0 1 0 2 3 2)", and the state frequencies to Equal. Build 49.

Bug Fixes
 * Many small bugs were fixed.
 * Current weights are now written into the NEXUS file for PAUP* runs.
 * In some contexts a character matrix is renamed when doing a Zephyr run. Fixed.

Version 1.1
New Features
 * Basic support for TNT added.
 * Improved support for PAUP*, including reconnectibility.

Bug Fixes
 * "Reconnectibility" had been accidentally broken just before the 1.0 release. You can now save a Mesquite file in the middle of a Zephyr run, close the file, open it sometime later, and it will reconnect to the Zephyr run.