Comments (4)
This line seems to be wrong, removing it seems to solve the first issue.
https://github.com/pranjalv123/ASTRID/blob/master/src/astrid.cpp#L223
But I still get the JAVA issue with bionj
from astrid.
Regarding the JAVA issue, I found a bypass.
The path here: https://github.com/pranjalv123/ASTRID/blob/master/src/DistanceMethods/phydstar.cpp#L45
is equal to
-Djava.class.path=/home/morelbt/.cache/bazel/_bazel_morelbt/5122b0a35d387e2057fb5506aa127b06/execroot/__main__/bazel-out/k8-opt/bin/src/PhyDstar.jar
The corresponding directory exists, but the jar file does not exist. I copied it from ASTRID/third_party/PhyDstar/PhyDstar.jar and it seems to work.
I don't know if something went wrong during the installation...
from astrid.
Hi Benoit,
I'm glad you were able to get it to work. I no longer recommend using PhyD* with ASTRID, partially because it gives worse results, and partially because it is difficult to configure properly.
The default ASTRID configuration should work with incomplete distance matrices and give you better results than you get with PhyD*.
from astrid.
Great, thanks for the advice :-)
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Related Issues (9)
- fatal build error: missing DistanceMatrix.hpp HOT 5
- Problem with bazel build //src:ASTRID-phydstar -c opt HOT 5
- Switching the default method for missing data to `-u -s` or `-u -n -s` HOT 3
- Expose UPGMA* as a standalone method
- `-u -n -s`, difference from `-u -s` HOT 1
- Remove experimental OCTAL support
- Error message in latest Mac OS X release HOT 3
- Potential memory leak during iterations
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