Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Changes for teiphy v0.1.20 #99

Closed
jjmccollum opened this issue Feb 3, 2025 · 0 comments · Fixed by #101
Closed

Changes for teiphy v0.1.20 #99

jjmccollum opened this issue Feb 3, 2025 · 0 comments · Fixed by #101
Assignees
Labels
enhancement New feature or request

Comments

@jjmccollum
Copy link
Owner

A number of changes are planned for the next minor release of teiphy, so I am using this issue to document them.

  • Cat Smith has graciously updated the dependencies and GitHub workflows to support up to Python 3.12. (This comes at the expense of support for Python 3.8, but that is nearing the end of its support period anyways.) Her fork at https://github.com/catsmith/teiphy should be merged into this repository.
  • To support Andrew Edmondson's extended version of MrBayes, the symbol set for MrBayes outputs should be extended to 64 symbols.
  • Support should be added for Phylip as an output format for distance/similarity matrices. An example follows:
10
P74     0.000000   7.837063  28.999559  15.763155  15.931898   5.878309  12.477022  10.253483  25.862832  10.991896
GA03    7.837063   0.000000  26.958600  13.555904  12.138728   5.195392  10.157400   7.191896  21.217410   8.100810
GA05    28.999559  26.958600   0.000000  27.016259  25.253821  26.142160  27.785030  25.805754  33.606213  25.786572
GA614   15.763155  13.555904  27.016259   0.000000   9.559471  12.262251  13.045429   9.956517  19.035780   9.696835
GA876   15.931898  12.138728  25.253821   9.559471   0.000000  12.255773  13.344463   9.547516  21.360369  10.019907
GA1175   5.878309   5.195392  26.142160  12.262251  12.255773   0.000000   8.492593   5.676071  21.385772   6.134831
GA1409  12.477022  10.157400  27.785030  13.045429  13.344463   8.492593   0.000000   8.474194  21.974661   8.144643
GA1739  10.253483   7.191896  25.805754   9.956517   9.547516   5.676071   8.474194   0.000000  20.325733   1.556377
GA1884  25.862832  21.217410  33.606213  19.035780  21.360369  21.385772  21.974661  20.325733   0.000000  20.178009
GA2200  10.991896   8.100810  25.786572   9.696835  10.019907   6.134831   8.144643   1.556377  20.178009   0.000000
@jjmccollum jjmccollum added the enhancement New feature or request label Feb 3, 2025
@jjmccollum jjmccollum self-assigned this Feb 3, 2025
@jjmccollum jjmccollum linked a pull request Feb 4, 2025 that will close this issue
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

Successfully merging a pull request may close this issue.

1 participant