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524D / compareMS2

Compare samples by MS2 spectra
MIT License
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Automatic MEGA run #22

Open magnuspalmblad opened 2 years ago

magnuspalmblad commented 2 years ago

Consider adding an option to the GUI, if a command-line version of MEGA is installed, that automatically generates a UPGMA tree with MEGA from the compareMS2 distance matrix.

The MEGA command-line version is available on https://www.megasoftware.net/ and can be launched with the following command:

megacc -a infer_UPGMA_distances.mao -d comp_distance_matrix.meg -o comp_UPGMA_tree

where "comp" is (or should be replaced with) the compareMS2 output filename root (in both places) and the "infer_UPGMA_distances.mao" is attached in the zip file below.

This creates a Newick file "comp_UPGMA_tree.nwk", which can of course be opened in MEGA (or any other software that read Newick files).

infer_UPGMA_distances.zip

524D commented 2 years ago

To start megacc without knowing its install location, the following can be used on Windows:

cmd /c start megacc -a infer_UPGMA_distances.mao -d comp_distance_matrix.meg -o comp_UPGMA_tree

It might also be nice to open the MEGA GUI directly from compareMS2 in a similar way (with mega_64 as the command to execute)