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phylen's Issues

TODO checklist

My TODO checklist

  • Add more parameters to control phylogenetic inference step. branch develop
  • Add more methods.
  • Change from super-gene phylogenetic inference to consensus from many alignments.
  • Apply "phylogenetic" algorithm to select between paralogues.
  • Add option or create new branch to take into account gene length when merging into orthologous groups. This will be useful to create cgMLST schemes.

Please add list of dependencies needed for installation

In assessing whether the package satisfies the installability criterion for openjournals/joss-reviews#593 I ran into a small road bump (I don't use phangorn, which is why this arose).

The install process halted with an error in installing igraph because of a lack of libxml2-dev on my system. It would be helpful for users if you provided a list of required system packages for each of the supported platforms since the R build systems are pretty unhelpful in pointing users in the right direction when things like this happen.

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