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iqtree / decenttree

Fast Neighbor-Joining and other distance-based methods for phylogenetics
GNU General Public License v2.0
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Installing and using via python #8

Open hyanwong opened 2 days ago

hyanwong commented 2 days ago

We would like a fast NJ implementation to use from python. I see there is a pydecenttree folder, but no instructions for installation. Indeed, there seem not to be any instructions from compilation from source either.

A pip install -e pydecenttree results in:

../utils/timeutil.h:28:10: fatal error: 'decenttree_config.h' file not found
    #include <decenttree_config.h>

(this is on a Mac)

hyanwong commented 2 days ago

I guess I need to first run cmake . in the root directory to produce the decenttree_config.h file. When I do that (on a Mac), and then try pip install -e pydecenttree I get:

        In file included from ../bionj2.cpp:54:
        In file included from ../upgma.h:102:
        ../vectorclass/vectorclass.h:38:4: error: Please compile for the SSE2 instruction set or higher
          #error Please compile for the SSE2 instruction set or higher
           ^
        In file included from ../bionj2.cpp:54:
        ../upgma.h:103:10: error: unknown type name 'Vec8f'
        typedef  Vec8f    FloatVector;
                 ^
        ../upgma.h:104:10: error: unknown type name 'Vec8fb'
        typedef  Vec8fb   FloatBoolVector;
                 ^