Calculate bin phylogeny

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Calculate bin phylogeny

For each .hmm file that targets translated aminoacid sequences, a phylogenetic tree is created based on concatenated alignments of all profiles in the file, that includes all reference taxa and bins.

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Runtime

Minutes.

External dependencies

This module requires MAFFT and FastTreeMP (You need the parallel version!).

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Parameters (type, default)

• Minimum profile extent for treeing (setMinimumProfileExtentForInclusion, int, 25): Only bins and reference genomes that cover (by default) at least 25% of all profiles in the .hmm file will be included in the tree.

• Set processors used (setProcessorsUsed, int, 4): The number of processors/cores/threads used for computations.

• Set temp folder (setTempFolder, String, "/temp/metawatt"): Temp folder used for intermediate files.

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Files generated

• ./output/[assemblyfilename][binset][.hmm filename].tree.newick: Inferred phylogenetic tree in newick format.