May 17, 2021 Announcement
We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation.
We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.
Examples of behavior that contributes to a positive environment for our community include:
Examples of unacceptable behavior include:
Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.
Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.
This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.
Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at m.bui(at)anu.edu.au. All complaints will be reviewed and investigated promptly and fairly.
All community leaders are obligated to respect the privacy and security of the reporter of any incident.
Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:
Community Impact: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.
Consequence: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.
Community Impact: A violation through a single incident or series of actions.
Consequence: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.
Community Impact: A serious violation of community standards, including sustained inappropriate behavior.
Consequence: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.
Community Impact: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals.
Consequence: A permanent ban from any sort of public interaction within the community.
This Code of Conduct is adapted from the Contributor Covenant, version 2.0, available at https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
Community Impact Guidelines were inspired by Mozilla’s code of conduct enforcement ladder.
Dec 12, 2019 Phd position
A PhD position is available in the lab of Dr. Minh Bui, https://researchers.anu.edu.au/researchers/bui-m, at the Research School of Computer Science, Australian National University (ANU). We are looking for a highly motivated student, who will work on the next generation of models and methods for phylogenetic analysis in the genomic era. There are a large number of potential directions that the research could take, and the details will depend on your interests and experience. Potential directions include: developing efficient algorithms for tree search; new approaches to phylogenetic model selection; co-estimating multiple trees. The student will implement new models and methods in the widely used IQ-TREE software (http://www.iqtree.org).
The ANU campus is situated in the heart of Australia’s capital city, Canberra, which is ranked as the third best city in the world according to Lonely Planet (2018) and is Australia’s most liveable city (Life in Australia Report 2019). The ANU has an international reputation for research excellence and is ranked among the best universities in the world (QS World University Ranking 2019).
Candidates: ANU scholarships are highly competitive, and cover all fees and a ~$27K stipend. In order to be put forward, you will need outstanding undergraduate marks and a first class honours or Masters by research (or be expecting to gain one by the middle of 2020) or equivalent research experience.
To apply, please send to m.bui (at) anu.edu.au a detailed CV, full academic transcripts, and a brief description of your research interests and how they intersect with this project.
The deadline is January 31, 2020.
Aug 15, 2019 Release
-ooption when the outgroup is identical to another sequence (reported by Yang Song).
-sppoption (reported by Bernardo Santos).
-supwhen target tree is not as “rooted/unrooted” as tree set (reported by Christian Rinke).
-ntoption) in Windows due to Clang compiler flag (reported by Wo Niu and others).
Jun 6, 2019 Release
-bnnioption and GENE/GENESITE resampling (reported by Emmanuel Cantu).
-bnnioption (reported by Max_IT).
Feb 19, 2019 Release
-bnnioption (reported by Mark Miller).
Dec 20, 2018 Release
-bnni(reported by Vanessa Vera Fain).
-rcluster-maxactivates relaxed clustering algorithm without having to specify
--no-outfilessuppress .treefile as expected (reported by Cecile Ane).
Oct 28, 2018 Release
Sep 7, 2018 Release
--show-lh(thanks Benjamin Redelings)
-st MULTIoption (requested by Ingo Ebersberger)
--runsand partition model (reported by David Maddison)
Aug 23, 2018 Release
-madd C10(reported by Juergen Strassert).
-bnnioption (reported by Juergen Strassert).
-m ..MERGE..wrong concatenateAlignments with missing data (reported by David Dunchene).
-bsamwith non-partition model (reported by Sarah Jensen).
Jul 1, 2018 Release
This version contains a number of bugfixes and is highly recommended for all users.
-lmapoption (reported by Giap Nguyen).
-bsam) for standard bootstrap (
-b) and jackknife (
-m ...MERGE) (reported by Guoqing Li).
-t RANDOM(reported by Karen Meusemann).