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Releases: hahnlab/CAFE5

1.1

17 Apr 15:43
@benfulton benfulton
v5.1
8d3ab08
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1.1 Latest
Latest

Added

  • The output file Base_report.cafe or Gamma_report.cafe has been added. This file has a
    format roughly the same as the CAFE 4 output, so tools and scripts that work with this
    format should run properly.
  • The tutorial now includes a cafe5_draw_tree.py script, demonstrating how to use BioPython
    to create a tree.

Changed

  • Ordering of nodes has changed. The order should now be the same, relative to the source Newick
    tree, as in the R package Ape.
  • The model_change.tab file no longer includes a "+" sign before positive change counts.
  • The simulator handles different max family and max root sizes correctly.
  • The DocTest unit tester has been updated to v2.4.9.
  • The application will no longer attempt to compute P-Values or a reconstruction, if the user
    specifies a lambda and the calculated -lnL is infinite.
  • The configure script now checks for the existence of mkl.h before attempting to use it.
  • Building the application should no longer fail if OpenMP is missing. (It will probably run
    much slower, however)
Assets 3
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Version 5.1 Beta

30 Mar 20:11
@benfulton benfulton
v5.1b
edd49e6
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Version 5.1 Beta Pre-release
Pre-release

[1.1.0] - 2023-03-30

Added

  • The output file Base_report.cafe or Gamma_report.cafe has been added. This file has a
    format roughly the same as the CAFE 4 output, so tools and scripts that work with this
    format should run properly.
  • The tutorial now includes a cafe5_draw_tree.py script, demonstrating how to use BioPython
    to create a tree.

Changed

  • Ordering of nodes has changed. The order should now be the same, relative to the source Newick
    tree, as in the R package Ape.
  • The model_change.tab file no longer includes a "+" sign before positive change counts.
  • The simulator handles different max family and max root sizes correctly.
  • The DocTest unit tester has been updated to v2.4.9.
  • The configure script now checks for the existence of mkl.h before attempting to use it.
  • Building the application should no longer fail if OpenMP is missing. (It will probably run
    much slower, however)
Assets 3

Initial Version 5 Release

30 Apr 17:32
@benfulton benfulton
v5.0
08d27a1
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Initial Version 5 Release

CAFE 5 is a new version of CAFE. Written entirely in C++, it is designed to provide a faster and more precise estimation of the lambda value by using a gamma rate to estimate the values. CAFE5 takes its arguments on the command line rather than in a script. See the README file for detailed instructions for use.

Assets 3

CAFE5 Initial Release (beta 2)

22 Jan 23:41
@benfulton benfulton
v5.0b2
c46f713
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CAFE5 Initial Release (beta 2) Pre-release
Pre-release

CAFE 5 is a new version of CAFE. Written entirely in C++, it is designed to provide a faster and more precise estimation of the lambda value by using a gamma rate to estimate the values. CAFE5 takes its arguments on the command line rather than in a script. See the README file for detailed instructions for use.

Beta 2:

  • Fixes an issue with the optimizer when including an error model
  • Fixes an issue incorrectly assigning significance to some branches of the tree
Assets 3

CAFE5 Initial Release (beta)

08 Jan 19:52
@benfulton benfulton
v5.0b
1eef213
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CAFE5 Initial Release (beta) Pre-release
Pre-release

CAFE 5 is a new version of CAFE. Written entirely in C++, it is designed to provide a faster and more precise estimation of the lambda value by using a gamma rate to estimate the values. CAFE5 takes its arguments on the command line rather than in a script. See the README file for detailed instructions for use.

Assets 3